- workflow update

- block adding tasks if pool is busy

.github/workflows/publish.yml

@@ -0,0 +1,31 @@
+name: Publish
+
+on: [workflow_dispatch]
+
+permissions:
+  contents: read
+
+jobs:
+  publish_pytest:
+    uses: ./.github/workflows/pytest.yml
+  pypi_publish:
+    runs-on: ubuntu-latest
+    needs: [ publish_pytest ]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6
+      - name: Build sdist
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+      - name: Install build
+        run: pip install build
+      - name: Build a binary wheel and a source tarball
+        run: python -m build
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          skip-existing: true
+          password: ${{ secrets.PYPI_API_TOKEN }}
+        env:
+          GITHUB_WORKFLOW_REF: 1.10.1

.github/workflows/publish_crates.yml

@@ -1,66 +0,0 @@
-name: Publish
-
-on: [workflow_dispatch]
-
-permissions:
-  contents: read
-
-jobs:
-  crates_io_publish:
-    name: Publish (crates.io)
-    runs-on: ubuntu-latest
-    timeout-minutes: 25
-    steps:
-      - uses: actions/checkout@v6
-      - name: Restore cache
-        uses: actions/cache/restore@v4
-        with:
-          path: |
-            ~/.cargo
-          key: cache-ubuntu-cargo-publish
-
-      - name: Install Rust
-        run: |-
-          export PATH="$HOME/.cargo/bin:$PATH"
-          if ! command -v rustc >/dev/null 2>&1; then
-            curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
-          else
-            rustup update
-          fi
-          cargo install cargo-release
-        shell: bash
-
-      # allow-branch HEAD is because GitHub actions switches
-      # to the tag while building, which is a detached head
-
-      # Publishing is currently messy, because:
-      #
-      # * `peace_rt_model_core` exports `NativeError` or `WebError` depending on the target.
-      # * `peace_rt_model_web` fails to build when publishing the workspace for a native target.
-      # * `peace_rt_model_web` still needs its dependencies to be published before it can be
-      #    published.
-      # * `peace_rt_model_hack` needs `peace_rt_model_web` to be published before it can be
-      #    published.
-      #
-      # We *could* pass through `--no-verify` so `cargo` doesn't build the crate before publishing,
-      # which is reasonable, since this job only runs after the Linux, Windows, and WASM builds
-      # have passed.
-      - name: "cargo release publish"
-        run: |-
-          export PATH="$HOME/.osxcross/bin:$PATH"
-          cargo login ${{ secrets.CRATES_IO_API_TOKEN }}
-          cargo release \
-            publish \
-            --workspace \
-            --all-features \
-            --allow-branch "main" \
-            --no-confirm \
-            --no-verify \
-            --execute
-
-      - name: Store cache
-        uses: actions/cache/save@v4
-        with:
-          path: |
-            ~/.cargo
-          key: cache-ubuntu-cargo-publish

.github/workflows/publish_pypi.yml

@@ -1,115 +0,0 @@
-name: CI
-
-on: [workflow_dispatch]
-
-permissions:
-  contents: read
-
-jobs:
-  pypi_publish:
-    name: Publish (pypi.org)
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v6
-      - uses: actions/setup-python@v5
-        with:
-          python-version: 3.x
-
-      - name: Restore cache
-        uses: actions/cache/restore@v4
-        with:
-          path: |
-            ~/.cache/pip
-            ~/.cache/pip-wheel
-            ~/.cache/sccache
-            ~/.cache/cargo-xwin
-            ~/.cargo
-            ~/.osxcross
-          key: cache-ubuntu-maturin-cross-compile
-
-      - name: Install llvm
-        run: |
-          if ! command -v llvm-dlltool >/dev/null 2>&1; then
-            sudo apt update
-            sudo apt install -y llvm
-          fi
-        shell: bash
-
-      - name: Install Rust
-        run: |
-          export PATH="$HOME/.cargo/bin:$PATH"
-          if ! command -v rustc >/dev/null 2>&1; then
-            curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
-          else
-            rustup update
-          fi
-        shell: bash
-
-      - name: Install sccache and maturin
-        run: |
-          export PATH="$HOME/.cargo/bin:$PATH"
-          python -m pip install --upgrade pip
-          pip install maturin ziglang
-          if ! command -v sccache >/dev/null 2>&1; then
-            cargo install sccache || pip install sccache
-          fi
-        shell: bash
-
-      - name: Install xwin
-        run: |
-          export PATH="$HOME/.cargo/bin:$PATH"
-          if ! command -v cargo-xwin >/dev/null 2>&1; then
-            cargo install cargo-xwin || pip install cargo-xwin
-            cargo xwin cache xwin
-          fi
-        shell: bash
-
-      - name: Install osxcross
-        run: |
-          export PATH="$HOME/.osxcross/bin:$PATH"
-          if ! command -v osxcross >/dev/null 2>&1; then
-            wget ${{ secrets.OSXCROSS_LINK }} -O osxcross.tar.gz
-            tar -xzf osxcross.tar.gz -C ~/
-            mv ~/osxcross ~/.osxcross
-          fi
-
-      - name: Build wheels
-        run: |
-          export PATH="$HOME/.cargo/bin:$HOME/.osxcross/bin:$PATH"
-          rm -rf dist
-          maturin sdist --out dist -m ome-metadata/Cargo.toml
-          rustup default nightly
-          
-          rustup target add x86_64-unknown-linux-gnu --toolchain nightly
-          maturin build --release --out ../dist --target x86_64-unknown-linux-gnu -m ome-metadata/Cargo.toml
-          rustup target add aarch64-unknown-linux-gnu --toolchain nightly
-          maturin build --release --out ../dist --target aarch64-unknown-linux-gnu --zig -m ome-metadata/Cargo.toml
-          
-          rustup target add x86_64-pc-windows-msvc --toolchain nightly
-          maturin build --release --out dist --target x86_64-pc-windows-msvc -m ome-metadata/Cargo.toml
-          rustup target add aarch64-pc-windows-msvc --toolchain nightly
-          maturin build --release --out dist --target aarch64-pc-windows-msvc -m ome-metadata/Cargo.toml
-          
-          rustup target add x86_64-apple-darwin --toolchain nightly
-          maturin build --release --out dist --target x86_64-apple-darwin --zig -m ome-metadata/Cargo.toml
-          rustup target add aarch64-apple-darwin --toolchain nightly
-          maturin build --release --out dist --target aarch64-apple-darwin --zig -m ome-metadata/Cargo.toml
-
-      - name: Store cache
-        uses: actions/cache/save@v4
-        with:
-          path: |
-            ~/.cache/pip
-            ~/.cache/pip-wheel
-            ~/.cache/sccache
-            ~/.cache/cargo-xwin
-            ~/.cargo
-            ~/.osxcross
-          key: cache-ubuntu-maturin-cross-compile
-
-      - name: Publish to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          password: ${{ secrets.PYPI_API_TOKEN }}
-        env:
-          GITHUB_WORKFLOW_REF: 1.10.1

.github/workflows/pytest.yml

@@ -0,0 +1,26 @@
+name: PyTest
+
+on: [push, pull_request, workflow_call]
+
+permissions:
+  contents: read
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ "3.10", "3.12", "3.14" ]
+        os: [ ubuntu-latest ]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install
+        run: pip install .[test]
+      - name: Test with pytest
+        run: pytest

.gitignore

@@ -1,76 +1,6 @@
-/target
+/build/
-
+/dist/
-# Byte-compiled / optimized / DLL files
+/parfor.egg-info/
-__pycache__/
+/.idea/
-.pytest_cache/
+/.pytest_cache/
-*.py[cod]
+._*
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-.venv/
-env/
-bin/
-build/
-develop-eggs/
-dist/
-eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-include/
-man/
-venv/
-*.egg-info/
-.installed.cfg
-*.egg
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-pip-selfcheck.json
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.coverage
-.cache
-nosetests.xml
-coverage.xml
-
-# Translations
-*.mo
-
-# Mr Developer
-.mr.developer.cfg
-.project
-.pydevproject
-
-# Rope
-.ropeproject
-
-# Django stuff:
-*.log
-*.pot
-
-.DS_Store
-
-# Sphinx documentation
-docs/_build/
-
-# PyCharm
-.idea/
-
-# VSCode
-.vscode/
-
-# Pyenv
-.python-version
-Cargo.lock
-target/
-
-.agentbridge

Cargo.toml

@@ -1,16 +0,0 @@
-[workspace]
-resolver = "3"
-members = ["ome-metadata", "ome-metadata-derive"]
-
-[workspace.package]
-version = "0.5.0"
-edition = "2024"
-rust-version = "1.88.0"
-authors = ["Wim Pomp <w.pomp@nki.nl>"]
-license = "MIT OR Apache-2.0"
-description = "Ome metadata as a rust/python structure."
-homepage = "https://git.pomppervova.nl/wim/ome-metadata"
-repository = "https://git.pomppervova.nl/wim/ome-metadata"
-readme = "README.md"
-keywords = ["bioformats", "imread", "ome", "metadata"]
-categories = ["multimedia::images", "science"]

LICENSE

@@ -0,0 +1,19 @@
+Copyright (c) 2025 Wim Pomp
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -1,25 +1,168 @@
-# ome-metadata
+[![pytest](https://git.wimpomp.nl/wim/parfor/actions/workflows/pytest.yml/badge.svg)](https://git.wimpomp.nl/wim/parfor/actions?workflow=pytest.yml)
 
-Open Microscopy XML metadata (https://www.openmicroscopy.org/Schemas/) as a collection of Rust structs and enums, with translation to Python.
+# Parfor
+Used to parallelize for-loops using parfor in Matlab? This package allows you to do the same in python.
+Take any normal serial but parallelizable for-loop and execute it in parallel using easy syntax.
+Don't worry about the technical details of using the multiprocessing module, race conditions, queues,
+parfor handles all that. Now powered by [ray](https://pypi.org/project/ray/).
 
-## Rust
+Tested on linux, Windows and OSX with python 3.10 and 3.12.
-``` 
-use std::fs::read_to_string;
-use ome_metadata::Ome;
 
-let xml = read_to_string($file)?;
+## Why is parfor better than just using multiprocessing?
-let ome: Ome = xml.parse()?;
+- Easy to use
-let image = &ome.image[0];
+- Progress bars are built-in
-println!("acquisition date: {:#?}", image.acquisition_date);
+- Retry the task in the main process upon failure for easy debugging
-```
+- Using a modified version of dill when ray fails to serialize an object: 
+  a lot more objects can be used when parallelizing
 
-## Python
+## How it works
-```
+[Ray](https://pypi.org/project/ray/) does all the heavy lifting. Parfor now is just a wrapper around ray, adding
-from ome_metadata import Ome
+some ergonomics.
 
-with open($file) as f:
+## Installation
-    xml = f.read()
+`pip install parfor`
-ome = Ome.from_xml(xml)
+
-image = ome.image[0]
+## Usage
-print(f"acquisition date: {image.acquisition_date}")
+Parfor decorates a functions and returns the result of that function evaluated in parallel for each iteration of
-```
+an iterator.
+
+## Requires
+numpy, ray, tqdm
+
+## Arguments
+To functions `parfor.parfor`, `parfor.pmap` and `parfor.gmap`.
+
+### Required:
+    fun:      function taking arguments: iteration from  iterable, other arguments defined in args & kwargs
+    iterable: iterable or iterator from which an item is given to fun as a first argument
+
+### Optional:
+    args:   tuple with other unnamed arguments to fun
+    kwargs: dict with other named arguments to fun
+    total:  give the length of the iterator in cases where len(iterator) results in an error
+    desc:   string with description of the progress bar
+    bar:    bool enable progress bar,
+                or a callback function taking the number of passed iterations as an argument
+    serial: execute in series instead of parallel if True, None (default): let pmap decide
+    n_processes: number of processes to use,
+        the parallel pool will be restarted if the current pool does not have the right number of processes
+    yield_ordered: return the result in the same order as the iterable
+    yield_index: return the index of the result too
+    allow_output: allow output from subprocesses
+    **bar_kwargs: keyword arguments for tqdm.tqdm
+
+### Return
+    list with results from applying the function 'fun' to each iteration of the iterable / iterator
+
+## Examples
+### Normal serial for loop
+    <<
+    from time import sleep
+
+    a = 3
+    fun = []
+    for i in range(10):
+        sleep(1)
+        fun.append(a * i ** 2)
+    print(fun)
+
+    >> [0, 3, 12, 27, 48, 75, 108, 147, 192, 243]
+    
+### Using parfor to parallelize
+    <<
+    from time import sleep
+    from parfor import parfor
+    @parfor(range(10), (3,))
+    def fun(i, a):
+        sleep(1)
+        return a * i ** 2
+    print(fun)
+
+    >> [0, 3, 12, 27, 48, 75, 108, 147, 192, 243]
+
+    <<
+    @parfor(range(10), (3,), bar=False)
+    def fun(i, a):
+        sleep(1)
+        return a * i ** 2
+    print(fun)
+
+    >> [0, 3, 12, 27, 48, 75, 108, 147, 192, 243]
+
+### Using parfor in a script/module/.py-file
+Parfor should never be executed during the import phase of a .py-file. To prevent that from happening
+use the `if __name__ == '__main__':` structure:
+
+    <<
+    from time import sleep
+    from parfor import parfor
+    
+    if __name__ == '__main__':
+        @parfor(range(10), (3,))
+        def fun(i, a):
+            sleep(1)
+            return a * i ** 2
+        print(fun)
+
+    >> [0, 3, 12, 27, 48, 75, 108, 147, 192, 243]    
+or:
+
+    <<
+    from time import sleep
+    from parfor import parfor
+    
+    def my_fun(*args, **kwargs):
+        @parfor(range(10), (3,))
+        def fun(i, a):
+            sleep(1)
+            return a * i ** 2
+        return fun
+    
+    if __name__ == '__main__':
+        print(my_fun())
+
+    >> [0, 3, 12, 27, 48, 75, 108, 147, 192, 243]
+
+### If you hate decorators not returning a function
+pmap maps an iterator to a function like map does, but in parallel
+
+    <<
+    from parfor import pmap
+    from time import sleep
+    def fun(i, a):
+        sleep(1)
+        return a * i ** 2
+    print(pmap(fun, range(10), (3,)))
+
+    >> [0, 3, 12, 27, 48, 75, 108, 147, 192, 243]     
+    
+### Using generators
+If iterators like lists and tuples are too big for the memory, use generators instead.
+Since generators don't have a predefined length, give parfor the length (total) as an argument (optional). 
+    
+    <<
+    import numpy as np
+    c = (im for im in imagereader)
+    @parfor(c, total=len(imagereader))
+    def fun(im):
+        return np.mean(im)
+        
+    >> [list with means of the images]
+    
+# Extra's
+## `pmap`
+The function parfor decorates, it's used similarly to `map`, it returns a list with the results.
+
+## `gmap`
+Same as pmap, but returns a generator. Useful to use the result as soon as it's generated.
+
+## `Chunks`
+Split a long iterator in bite-sized chunks to parallelize
+
+## `ParPool`
+More low-level accessibility to parallel execution. Submit tasks and request the result at any time,
+(although to avoid breaking causality, submit first, then request), use different functions and function
+arguments for different tasks.
+
+## `SharedArray`
+A numpy arrow that can be shared among processes.

ome-metadata-derive/Cargo.toml

@@ -1,11 +0,0 @@
-[package]
-name = "ome-metadata-derive"
-version = "0.5.0"
-edition = "2024"
-
-[dependencies]
-quote = "1"
-syn = "2"
-
-[lib]
-proc-macro = true

ome-metadata-derive/LICENSE-APACHE

@@ -1,201 +0,0 @@
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-                        Version 2.0, January 2004
-                     http://www.apache.org/licenses/
-
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-
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-   outstanding shares, or (iii) beneficial ownership of such entity.
-
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-   agreed to in writing, Licensor provides the Work (and each
-   Contributor provides its Contributions) on an "AS IS" BASIS,
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-   PARTICULAR PURPOSE. You are solely responsible for determining the
-   appropriateness of using or redistributing the Work and assume any
-   risks associated with Your exercise of permissions under this License.
-
-8. Limitation of Liability. In no event and under no legal theory,
-   whether in tort (including negligence), contract, or otherwise,
-   unless required by applicable law (such as deliberate and grossly
-   negligent acts) or agreed to in writing, shall any Contributor be
-   liable to You for damages, including any direct, indirect, special,
-   incidental, or consequential damages of any character arising as a
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-   work stoppage, computer failure or malfunction, or any and all
-   other commercial damages or losses), even if such Contributor
-   has been advised of the possibility of such damages.
-
-9. Accepting Warranty or Additional Liability. While redistributing
-   the Work or Derivative Works thereof, You may choose to offer,
-   and charge a fee for, acceptance of support, warranty, indemnity,
-   or other liability obligations and/or rights consistent with this
-   License. However, in accepting such obligations, You may act only
-   on Your own behalf and on Your sole responsibility, not on behalf
-   of any other Contributor, and only if You agree to indemnify,
-   defend, and hold each Contributor harmless for any liability
-   incurred by, or claims asserted against, such Contributor by reason
-   of your accepting any such warranty or additional liability.
-
-END OF TERMS AND CONDITIONS
-
-APPENDIX: How to apply the Apache License to your work.
-
-   To apply the Apache License to your work, attach the following
-   boilerplate notice, with the fields enclosed by brackets "[]"
-   replaced with your own identifying information. (Don't include
-   the brackets!)  The text should be enclosed in the appropriate
-   comment syntax for the file format. We also recommend that a
-   file or class name and description of purpose be included on the
-   same "printed page" as the copyright notice for easier
-   identification within third-party archives.
-
-Copyright [yyyy] [name of copyright owner]
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
-	http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.

ome-metadata-derive/LICENSE-MIT

@@ -1,27 +0,0 @@
-Copyright (c) 2015 - 2021 Ulrik Sverdrup "bluss",
-			  Jim Turner,
-			  and ndarray developers
-
-Permission is hereby granted, free of charge, to any
-person obtaining a copy of this software and associated
-documentation files (the "Software"), to deal in the
-Software without restriction, including without
-limitation the rights to use, copy, modify, merge,
-publish, distribute, sublicense, and/or sell copies of
-the Software, and to permit persons to whom the Software
-is furnished to do so, subject to the following
-conditions:
-
-The above copyright notice and this permission notice
-shall be included in all copies or substantial portions
-of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF
-ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED
-TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
-PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT
-SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
-CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
-OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR
-IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
-DEALINGS IN THE SOFTWARE.

ome-metadata-derive/README.md

@@ -1 +0,0 @@
-# Derive macros for ome-metadata

ome-metadata-derive/src/lib.rs

@@ -1,297 +0,0 @@
-use proc_macro::TokenStream;
-use quote::quote;
-use syn::{Data, DeriveInput, Fields, Visibility, parse_macro_input};
-
-#[proc_macro_derive(OmeXML)]
-pub fn ome_metadata_derive_xml(input: TokenStream) -> TokenStream {
-    let input = parse_macro_input!(input as DeriveInput);
-    let ident = input.ident;
-
-    let expanded = quote! {
-        impl #ident {
-            pub fn from_xml<T: AsRef<str>>(s: T) -> Result<Self, Error> {
-                Ok(from_str(s.as_ref())?)
-            }
-
-            pub fn to_xml(&self) -> Result<String, Error> {
-                Ok(to_string(self)?)
-            }
-        }
-    };
-
-    TokenStream::from(expanded)
-}
-
-#[proc_macro_derive(PyOmeComplexEnum)]
-pub fn ome_metadata_derive_complex_enum(input: TokenStream) -> TokenStream {
-    let input = parse_macro_input!(input as DeriveInput);
-    let ident = input.ident;
-
-    let mut variants = Vec::new();
-
-    match input.data {
-        Data::Enum(s) => {
-            for variant in &s.variants {
-                let variant_ident = &variant.ident;
-                variants.push(quote! {
-                    Self::#variant_ident(v) => v.clone().into_bound_py_any(py)?,
-                });
-            }
-        }
-        _ => {
-            return syn::Error::new_spanned(ident, "PyOmeComplexEnum only supports structs")
-                .to_compile_error()
-                .into();
-        }
-    };
-
-    let expanded = quote! {
-        impl PyDisplay for #ident {
-            fn py_str(&self) -> String {
-                format!("{:?}", self)
-            }
-        }
-
-        #[pyo3::prelude::pymethods]
-        impl #ident {
-            /// all possible variants of this enum that can be constructed or converted into
-            #[staticmethod]
-            fn variants() -> Vec<String> {
-                Self::VARIANTS.iter().map(|v| v.trim_matches('"').to_string()).collect()
-            }
-
-            fn __repr__(&self) -> String {
-                self.py_str()
-            }
-
-            fn __str__(&self) -> String {
-                self.py_str()
-            }
-
-            fn __getnewargs__<'py>(&self, py: Python<'py>) -> PyResult<(Bound<'py, PyAny>,)> {
-                Ok((match self { #(#variants)* },))
-            }
-
-            #[staticmethod]
-            #[pyo3(name = "from_xml")]
-            fn py_from_xml(xml: &str) -> PyResult<Self> {
-                Ok(Self::from_xml(xml)?)
-            }
-
-            #[pyo3(name = "to_xml")]
-            fn py_to_xml(&self) -> PyResult<String> {
-                Ok(self.to_xml()?)
-            }
-        }
-    };
-
-    TokenStream::from(expanded)
-}
-
-#[proc_macro_derive(PyOmeEnum)]
-pub fn ome_metadata_derive_enum(input: TokenStream) -> TokenStream {
-    let input = parse_macro_input!(input as DeriveInput);
-    let name = input.ident;
-
-    let expanded = quote! {
-        impl PyDisplay for #name {
-            fn py_str(&self) -> String {
-                format!("{}", self)
-            }
-        }
-
-        #[pyo3::prelude::pymethods]
-        impl #name {
-            #[new]
-            fn new(unit: &str) -> PyResult<Self> {
-                unit.parse().map_err(|_| PyErr::new::<pyo3::exceptions::PyValueError, _>(format!("could not parse {}", unit)))
-            }
-
-            /// all possible variants of this enum that can be constructed or converted into
-            #[staticmethod]
-            fn variants() -> Vec<String> {
-                Self::VARIANTS.iter().map(|v| v.trim_matches('"').to_string()).collect()
-            }
-
-            fn __repr__(&self) -> String {
-                self.py_str()
-            }
-
-            fn __str__(&self) -> String {
-                self.py_str()
-            }
-
-            fn __getnewargs__(&self) -> (String,) {
-                (format!("{}", self),)
-            }
-
-            #[staticmethod]
-            #[pyo3(name = "from_xml")]
-            fn py_from_xml(xml: &str) -> PyResult<Self> {
-                Ok(Self::from_xml(xml)?)
-            }
-
-            #[pyo3(name = "to_xml")]
-            fn py_to_xml(&self) -> PyResult<String> {
-                Ok(self.to_xml()?)
-            }
-        }
-    };
-
-    TokenStream::from(expanded)
-}
-
-#[proc_macro_derive(PyOmeUnit)]
-pub fn ome_metadata_derive_unit(input: TokenStream) -> TokenStream {
-    let input = parse_macro_input!(input as DeriveInput);
-    let name = input.ident;
-
-    let expanded = quote! {
-        impl PyDisplay for #name {
-            fn py_str(&self) -> String {
-                format!("{}", self)
-            }
-        }
-
-        #[pyo3::prelude::pymethods]
-        impl #name {
-            #[new]
-            fn new(unit: &str) -> PyResult<Self> {
-                unit.parse().map_err(|_| PyErr::new::<pyo3::exceptions::PyValueError, _>(format!("could not parse {}", unit)))
-            }
-
-            /// convert a value between units
-            #[pyo3(name = "convert")]
-            fn py_convert(&self, unit: &Self, value: f64) -> PyResult<f64> {
-                Ok(self.convert(unit, value)?)
-            }
-
-            /// all possible variants of this enum that can be constructed or converted into
-            #[staticmethod]
-            fn variants() -> Vec<String> {
-                Self::VARIANTS.iter().map(|v| v.trim_matches('"').to_string()).collect()
-            }
-
-            fn __repr__(&self) -> String {
-                self.py_str()
-            }
-
-            fn __str__(&self) -> String {
-                self.py_str()
-            }
-
-            fn __getnewargs__(&self) -> (String,) {
-                (format!("{}", self),)
-            }
-
-            #[staticmethod]
-            #[pyo3(name = "from_xml")]
-            fn py_from_xml(xml: &str) -> PyResult<Self> {
-                Ok(Self::from_xml(xml)?)
-            }
-
-            #[pyo3(name = "to_xml")]
-            fn py_to_xml(&self) -> PyResult<String> {
-                Ok(self.to_xml()?)
-            }
-        }
-    };
-
-    TokenStream::from(expanded)
-}
-
-#[proc_macro_derive(PyOme)]
-pub fn ome_metadata_derive(input: TokenStream) -> TokenStream {
-    let input = parse_macro_input!(input as DeriveInput);
-    let name = input.ident;
-
-    // Only support named structs
-    let fields = match input.data {
-        Data::Struct(s) => match s.fields {
-            Fields::Named(named) => named.named,
-            _ => {
-                return syn::Error::new_spanned(name, "PyOme only supports named structs")
-                    .to_compile_error()
-                    .into();
-            }
-        },
-        _ => {
-            return syn::Error::new_spanned(name, "PyOme only supports structs")
-                .to_compile_error()
-                .into();
-        }
-    };
-
-    let mut idents = Vec::new();
-    let mut types = Vec::new();
-    let mut f = Vec::new();
-    let mut ps = Vec::new();
-    let mut new_kwargs = Vec::new();
-    let mut s = Vec::new();
-
-    for field in fields.iter() {
-        let ty = &field.ty;
-        if let Some(ident) = &field.ident
-            && let Visibility::Public(_) = field.vis
-        {
-            let tmp = ident.to_string();
-            let field_name = tmp.trim_start_matches("r#");
-            idents.push(quote! {
-                self.#ident
-            });
-            types.push(quote! { #ty });
-            f.push(quote! {
-                pub #ident: #ty
-            });
-            ps.push(quote! {
-                self.#ident.py_str()
-            });
-            new_kwargs.push(quote! {
-                (#field_name, self.#ident.clone().into_bound_py_any(py)?)
-            });
-            s.push(format!("{}: {{}}", field_name));
-        } else {
-            return syn::Error::new_spanned(field, "PyOme type only supports public named fields")
-                .to_compile_error()
-                .into();
-        }
-    }
-    let fmt = format!("{}({})", name, s.join(", "));
-
-    // Generate the token stream
-    let expanded = quote! {
-        impl PyDisplay for #name {
-            fn py_str(&self) -> String {
-                format!(#fmt, #(#ps,)*)
-            }
-        }
-
-        #[pyo3::prelude::pymethods]
-        impl #name {
-            fn __getnewargs_ex__<'py>(&self, py: Python<'py>) -> PyResult<((), std::collections::HashMap<&str, Bound<'py, PyAny>>)> {
-                Ok(((), std::collections::HashMap::from_iter([#(#new_kwargs,)*])))
-            }
-
-            fn __repr__(&self) -> String {
-                self.py_str()
-            }
-
-            fn __str__(&self) -> String {
-                self.py_str()
-            }
-
-            #[staticmethod]
-            #[pyo3(name = "from_xml")]
-            fn py_from_xml(xml: &str) -> PyResult<Self> {
-                Ok(Self::from_xml(xml)?)
-            }
-
-            #[pyo3(name = "to_xml")]
-            fn py_to_xml(&self) -> PyResult<String> {
-                Ok(self.to_xml()?)
-            }
-        }
-    };
-
-    TokenStream::from(expanded)
-}

ome-metadata/Cargo.toml

@@ -1,32 +0,0 @@
-[package]
-name = "ome-metadata"
-version = "0.5.0"
-edition = "2024"
-rust-version = "1.88.0"
-authors = ["Wim Pomp <w.pomp@nki.nl>"]
-license = "MIT OR Apache-2.0"
-description = "Ome metadata as a rust/python structure."
-homepage = "https://git.pomppervova.nl/wim/ome-metadata"
-repository = "https://git.pomppervova.nl/wim/ome-metadata"
-documentation = "https://docs.rs/ome-metadata"
-readme = "README.md"
-keywords = ["bioformats", "imread", "ome", "metadata"]
-categories = ["multimedia::images", "science"]
-exclude = ["/tests"]
-
-# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
-[lib]
-name = "ome_metadata"
-crate-type = ["cdylib", "rlib"]
-
-[dependencies]
-color-eyre = { version = "0.6", optional = true }
-ome-metadata-derive = { path = "../ome-metadata-derive" }
-pyo3 = { version = "0.29", features = ["abi3-py310", "anyhow", "eyre", "generate-import-lib"], optional = true}
-quick-xml = { version = "0.40", features = ["serialize"] }
-serde = { version = "1", features = ["derive"] }
-strum = { version = "0.28", features = ["derive"] }
-thiserror = "2"
-
-[features]
-python = ["dep:pyo3", "dep:color-eyre"]

ome-metadata/LICENSE-APACHE

@@ -1,201 +0,0 @@
-                              Apache License
-                        Version 2.0, January 2004
-                     http://www.apache.org/licenses/
-
-TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
-
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-
-   "License" shall mean the terms and conditions for use, reproduction,
-   and distribution as defined by Sections 1 through 9 of this document.
-
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-   the copyright owner that is granting the License.
-
-   "Legal Entity" shall mean the union of the acting entity and all
-   other entities that control, are controlled by, or are under common
-   control with that entity. For the purposes of this definition,
-   "control" means (i) the power, direct or indirect, to cause the
-   direction or management of such entity, whether by contract or
-   otherwise, or (ii) ownership of fifty percent (50%) or more of the
-   outstanding shares, or (iii) beneficial ownership of such entity.
-
-   "You" (or "Your") shall mean an individual or Legal Entity
-   exercising permissions granted by this License.
-
-   "Source" form shall mean the preferred form for making modifications,
-   including but not limited to software source code, documentation
-   source, and configuration files.
-
-   "Object" form shall mean any form resulting from mechanical
-   transformation or translation of a Source form, including but
-   not limited to compiled object code, generated documentation,
-   and conversions to other media types.
-
-   "Work" shall mean the work of authorship, whether in Source or
-   Object form, made available under the License, as indicated by a
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-   (an example is provided in the Appendix below).
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-   editorial revisions, annotations, elaborations, or other modifications
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-   the terms of any separate license agreement you may have executed
-   with Licensor regarding such Contributions.
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-
-7. Disclaimer of Warranty. Unless required by applicable law or
-   agreed to in writing, Licensor provides the Work (and each
-   Contributor provides its Contributions) on an "AS IS" BASIS,
-   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
-   implied, including, without limitation, any warranties or conditions
-   of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
-   PARTICULAR PURPOSE. You are solely responsible for determining the
-   appropriateness of using or redistributing the Work and assume any
-   risks associated with Your exercise of permissions under this License.
-
-8. Limitation of Liability. In no event and under no legal theory,
-   whether in tort (including negligence), contract, or otherwise,
-   unless required by applicable law (such as deliberate and grossly
-   negligent acts) or agreed to in writing, shall any Contributor be
-   liable to You for damages, including any direct, indirect, special,
-   incidental, or consequential damages of any character arising as a
-   result of this License or out of the use or inability to use the
-   Work (including but not limited to damages for loss of goodwill,
-   work stoppage, computer failure or malfunction, or any and all
-   other commercial damages or losses), even if such Contributor
-   has been advised of the possibility of such damages.
-
-9. Accepting Warranty or Additional Liability. While redistributing
-   the Work or Derivative Works thereof, You may choose to offer,
-   and charge a fee for, acceptance of support, warranty, indemnity,
-   or other liability obligations and/or rights consistent with this
-   License. However, in accepting such obligations, You may act only
-   on Your own behalf and on Your sole responsibility, not on behalf
-   of any other Contributor, and only if You agree to indemnify,
-   defend, and hold each Contributor harmless for any liability
-   incurred by, or claims asserted against, such Contributor by reason
-   of your accepting any such warranty or additional liability.
-
-END OF TERMS AND CONDITIONS
-
-APPENDIX: How to apply the Apache License to your work.
-
-   To apply the Apache License to your work, attach the following
-   boilerplate notice, with the fields enclosed by brackets "[]"
-   replaced with your own identifying information. (Don't include
-   the brackets!)  The text should be enclosed in the appropriate
-   comment syntax for the file format. We also recommend that a
-   file or class name and description of purpose be included on the
-   same "printed page" as the copyright notice for easier
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-Copyright [yyyy] [name of copyright owner]
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-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
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-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.

ome-metadata/LICENSE-MIT

@@ -1,27 +0,0 @@
-Copyright (c) 2015 - 2021 Ulrik Sverdrup "bluss",
-			  Jim Turner,
-			  and ndarray developers
-
-Permission is hereby granted, free of charge, to any
-person obtaining a copy of this software and associated
-documentation files (the "Software"), to deal in the
-Software without restriction, including without
-limitation the rights to use, copy, modify, merge,
-publish, distribute, sublicense, and/or sell copies of
-the Software, and to permit persons to whom the Software
-is furnished to do so, subject to the following
-conditions:
-
-The above copyright notice and this permission notice
-shall be included in all copies or substantial portions
-of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF
-ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED
-TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
-PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT
-SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
-CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
-OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR
-IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
-DEALINGS IN THE SOFTWARE.

ome-metadata/README.md

@@ -1,25 +0,0 @@
-# ome-metadata
-
-Open Microscopy XML metadata (https://www.openmicroscopy.org/Schemas/) as a collection of Rust structs and enums, with translation to Python.
-
-## Rust
-``` 
-use std::fs::read_to_string;
-use ome_metadata::Ome;
-
-let xml = read_to_string($file)?;
-let ome: Ome = xml.parse()?;
-let image = &ome.image[0];
-println!("acquisition date: {:#?}", image.acquisition_date);
-```
-
-## Python
-```
-from ome_metadata import Ome
-
-with open($file) as f:
-    xml = f.read()
-ome = Ome.from_xml(xml)
-image = ome.image[0]
-print(f"acquisition date: {image.acquisition_date}")
-```

ome-metadata/pyproject.toml

@@ -1,33 +0,0 @@
-[build-system]
-requires = ["maturin>=1.9.4,<2.0"]
-build-backend = "maturin"
-
-[project]
-name = "ome-metadata"
-requires-python = ">=3.10"
-classifiers = [
-    "License :: OSI Approved :: MIT License",
-    "License :: OSI Approved :: Apache Software License",
-    "Programming Language :: Rust",
-    "Programming Language :: Python",
-    "Programming Language :: Python :: 3",
-]
-dynamic = [
-    "version",
-    "description",
-    "readme",
-    "license",
-    "license-files",
-    "authors",
-    "maintainers",
-    "keywords",
-    "urls",
-]
-
-[tool.maturin]
-features = ["python"]
-module-name = "ome_metadata"
-strip = true
-
-[tool.isort]
-line_length = 119

ome-metadata/src/error.rs

@@ -1,15 +0,0 @@
-use thiserror::Error;
-
-#[derive(Debug, Error)]
-pub enum Error {
-    #[error(transparent)]
-    IO(#[from] std::io::Error),
-    #[error(transparent)]
-    XmlDe(#[from] quick_xml::DeError),
-    #[error(transparent)]
-    XmlSe(#[from] quick_xml::SeError),
-    #[error("size of {0} is unknown")]
-    SizeOfUnknown(String),
-    #[error("no conversion to K by multiplication only")]
-    TemparatureConversion,
-}

ome-metadata/src/lib.rs

@@ -1,44 +0,0 @@
-#![allow(non_camel_case_types)]
-pub mod ome;
-
-pub mod error;
-#[cfg(feature = "python")]
-pub mod py;
-
-pub use ome::Ome;
-
-#[cfg(test)]
-mod tests {
-    use crate::Ome;
-    use crate::error::Error;
-    use std::fs::read_to_string;
-
-    macro_rules! test_read {
-        ($($name:ident: $file:expr $(,)?)*) => {
-            $(
-                #[test]
-                fn $name() -> Result<(), Error> {
-                    let file = read_to_string(format!("tests/{}.xml", $file))?;
-                    let ome = Ome::from_xml(file)?;
-                    let _xml = ome.to_xml()?;
-                    Ok(())
-                }
-            )*
-        };
-    }
-
-    test_read!(
-        a: "YTL1849A111_2023_05_04__14_46_19_cellnr_1_track"
-        b: "Experiment-2029"
-        c: "test"
-        d: "4-Pos_001_002"
-        e: "YTL1841B2-2-1_1hr_DMSO_galinduction_1"
-        f: "1xp53-01-AP1"
-        g: "YTL378_JF552"
-        h: "MK022_cE9_1-01-Airyscan Processing-01-Scene-2-P1"
-        i: "beads_2023_05_04__19_00_22"
-        j: "20230511-p53-4x-CMV-1min-4h-01-Airyscan Processing-01"
-        k: "YTL1849A131_2023_05_04__13_36_36"
-        l: "multi-channel.ome"
-    );
-}

ome-metadata/src/py.rs

@@ -1,487 +0,0 @@
-use crate::error::Error;
-use crate::ome::{ExperimentType, MetadataOnly, MicrobeamManipulationType, XmlAnnotationValue};
-use pyo3::prelude::*;
-use pyo3::types::PyTuple;
-
-impl From<crate::error::Error> for PyErr {
-    fn from(err: crate::error::Error) -> PyErr {
-        color_eyre::eyre::Report::from(err).into()
-    }
-}
-
-pub(crate) trait PyDisplay {
-    fn py_str(&self) -> String;
-}
-
-impl PyDisplay for String {
-    fn py_str(&self) -> String {
-        self.clone()
-    }
-}
-
-impl PyDisplay for bool {
-    fn py_str(&self) -> String {
-        self.to_string()
-    }
-}
-
-impl PyDisplay for i32 {
-    fn py_str(&self) -> String {
-        self.to_string()
-    }
-}
-impl PyDisplay for i64 {
-    fn py_str(&self) -> String {
-        self.to_string()
-    }
-}
-impl PyDisplay for f32 {
-    fn py_str(&self) -> String {
-        self.to_string()
-    }
-}
-impl PyDisplay for f64 {
-    fn py_str(&self) -> String {
-        self.to_string()
-    }
-}
-impl<T> PyDisplay for Option<T>
-where
-    T: PyDisplay,
-{
-    fn py_str(&self) -> String {
-        if let Some(val) = self {
-            val.py_str()
-        } else {
-            "None".to_string()
-        }
-    }
-}
-
-impl<T> PyDisplay for Vec<T>
-where
-    T: PyDisplay,
-{
-    fn py_str(&self) -> String {
-        format!(
-            "[{}]",
-            self.iter()
-                .map(|x| x.py_str())
-                .collect::<Vec<_>>()
-                .join(", ")
-        )
-    }
-}
-impl PyDisplay for MetadataOnly {
-    fn py_str(&self) -> String {
-        "MetadataOnly".into()
-    }
-}
-impl<'a, 'py> FromPyObject<'a, 'py> for MetadataOnly {
-    type Error = Error;
-
-    fn extract(_obj: Borrowed<'a, 'py, PyAny>) -> Result<Self, Self::Error> {
-        Ok(Self {})
-    }
-}
-impl PyDisplay for MicrobeamManipulationType {
-    fn py_str(&self) -> String {
-        format!(
-            "[{}]",
-            self.0
-                .iter()
-                .map(|i| i.py_str())
-                .collect::<Vec<_>>()
-                .join(", ")
-        )
-    }
-}
-impl<'a, 'py> FromPyObject<'a, 'py> for XmlAnnotationValue {
-    type Error = Error;
-
-    fn extract(_obj: Borrowed<'a, 'py, PyAny>) -> Result<Self, Self::Error> {
-        Ok(Self {})
-    }
-}
-impl PyDisplay for XmlAnnotationValue {
-    fn py_str(&self) -> String {
-        "XmlAnnotationValue".to_string()
-    }
-}
-impl PyDisplay for ExperimentType {
-    fn py_str(&self) -> String {
-        format!(
-            "[{}]",
-            self.0
-                .iter()
-                .map(|i| i.py_str())
-                .collect::<Vec<_>>()
-                .join(", ")
-        )
-    }
-}
-
-#[pymethods]
-impl MetadataOnly {
-    fn __getnewargs__<'py>(&self, py: Python<'py>) -> Bound<'py, PyTuple> {
-        PyTuple::empty(py)
-    }
-    fn __repr__(&self) -> String {
-        "MetadataOnly".into()
-    }
-    fn __str__(&self) -> String {
-        "MetadataOnly".into()
-    }
-}
-
-#[pyfunction]
-fn parse_ome(text: &str) -> PyResult<crate::Ome> {
-    Ok(crate::ome::Ome::from_xml(text)?)
-}
-
-#[pyfunction]
-fn to_xml(ome: crate::ome::Ome) -> PyResult<String> {
-    Ok(ome.to_xml()?)
-}
-
-#[pymodule]
-#[pyo3(name = "ome_metadata")]
-pub mod ome_metadata {
-    use pyo3::prelude::*;
-
-    #[pymodule_export]
-    use super::parse_ome;
-
-    #[pymodule_export]
-    use super::to_xml;
-
-    #[pymodule_export]
-    use crate::ome::AffineTransform;
-
-    #[pymodule_export]
-    use crate::ome::Annotation;
-
-    #[pymodule_export]
-    use crate::ome::AnnotationRef;
-
-    #[pymodule_export]
-    use crate::ome::Arc;
-
-    #[pymodule_export]
-    use crate::ome::BinData;
-
-    #[pymodule_export]
-    use crate::ome::BinaryFile;
-
-    #[pymodule_export]
-    use crate::ome::BooleanAnnotation;
-
-    #[pymodule_export]
-    use crate::ome::Channel;
-
-    #[pymodule_export]
-    use crate::ome::CommentAnnotation;
-
-    #[pymodule_export]
-    use crate::ome::Dataset;
-
-    #[pymodule_export]
-    use crate::ome::Detector;
-
-    #[pymodule_export]
-    use crate::ome::DetectorSettings;
-
-    #[pymodule_export]
-    use crate::ome::Dichroic;
-
-    #[pymodule_export]
-    use crate::ome::DoubleAnnotation;
-
-    #[pymodule_export]
-    use crate::ome::Ellipse;
-
-    #[pymodule_export]
-    use crate::ome::Experiment;
-
-    #[pymodule_export]
-    use crate::ome::ExperimentType;
-
-    #[pymodule_export]
-    use crate::ome::Experimenter;
-
-    #[pymodule_export]
-    use crate::ome::ExperimenterGroup;
-
-    #[pymodule_export]
-    use crate::ome::External;
-
-    #[pymodule_export]
-    use crate::ome::Filament;
-
-    #[pymodule_export]
-    use crate::ome::FileAnnotation;
-
-    #[pymodule_export]
-    use crate::ome::Filter;
-
-    #[pymodule_export]
-    use crate::ome::FilterSet;
-
-    #[pymodule_export]
-    use crate::ome::Folder;
-
-    #[pymodule_export]
-    use crate::ome::GenericExcitationSource;
-
-    #[pymodule_export]
-    use crate::ome::Image;
-
-    #[pymodule_export]
-    use crate::ome::ImagingEnvironment;
-
-    #[pymodule_export]
-    use crate::ome::Instrument;
-
-    #[pymodule_export]
-    use crate::ome::Label;
-
-    #[pymodule_export]
-    use crate::ome::Laser;
-
-    #[pymodule_export]
-    use crate::ome::LightEmittingDiode;
-
-    #[pymodule_export]
-    use crate::ome::LightPath;
-
-    #[pymodule_export]
-    use crate::ome::LightSourceType;
-
-    #[pymodule_export]
-    use crate::ome::LightSourceSettings;
-
-    #[pymodule_export]
-    use crate::ome::Line;
-
-    #[pymodule_export]
-    use crate::ome::LongAnnotation;
-
-    #[pymodule_export]
-    use crate::ome::MapType;
-
-    #[pymodule_export]
-    use crate::ome::MapAnnotation;
-
-    #[pymodule_export]
-    use crate::ome::MapM;
-
-    #[pymodule_export]
-    use crate::ome::Mask;
-
-    #[pymodule_export]
-    use crate::ome::MetadataOnly;
-
-    #[pymodule_export]
-    use crate::ome::MicrobeamManipulation;
-
-    #[pymodule_export]
-    use crate::ome::MicrobeamManipulationType;
-
-    #[pymodule_export]
-    use crate::ome::Microscope;
-
-    #[pymodule_export]
-    use crate::ome::Ome;
-
-    #[pymodule_export]
-    use crate::ome::Objective;
-
-    #[pymodule_export]
-    use crate::ome::ObjectiveSettings;
-
-    #[pymodule_export]
-    use crate::ome::OmeBinaryOnly;
-
-    #[pymodule_export]
-    use crate::ome::Pixels;
-
-    #[pymodule_export]
-    use crate::ome::Plane;
-
-    #[pymodule_export]
-    use crate::ome::Plate;
-
-    #[pymodule_export]
-    use crate::ome::PlateAcquisition;
-
-    #[pymodule_export]
-    use crate::ome::Polygon;
-
-    #[pymodule_export]
-    use crate::ome::Polyline;
-
-    #[pymodule_export]
-    use crate::ome::Project;
-
-    #[pymodule_export]
-    use crate::ome::Roi;
-
-    #[pymodule_export]
-    use crate::ome::Reagent;
-
-    #[pymodule_export]
-    use crate::ome::Rectangle;
-
-    #[pymodule_export]
-    use crate::ome::Rights;
-
-    #[pymodule_export]
-    use crate::ome::RoiUnion;
-
-    #[pymodule_export]
-    use crate::ome::Screen;
-
-    #[pymodule_export]
-    use crate::ome::ShapeType;
-
-    #[pymodule_export]
-    use crate::ome::StageLabel;
-
-    #[pymodule_export]
-    use crate::ome::StructuredAnnotations;
-
-    #[pymodule_export]
-    use crate::ome::TiffData;
-
-    #[pymodule_export]
-    use crate::ome::TiffDataUuid;
-
-    #[pymodule_export]
-    use crate::ome::TransmittanceRange;
-
-    #[pymodule_export]
-    use crate::ome::Well;
-
-    #[pymodule_export]
-    use crate::ome::WellSample;
-
-    #[pymodule_export]
-    use crate::ome::XmlAnnotation;
-
-    #[pymodule_export]
-    use crate::ome::XmlAnnotationValue;
-
-    #[pymodule_export]
-    use crate::ome::ArcType;
-
-    #[pymodule_export]
-    use crate::ome::BinDataCompressionType;
-
-    #[pymodule_export]
-    use crate::ome::BinaryFileContent;
-
-    #[pymodule_export]
-    use crate::ome::BinningType;
-
-    #[pymodule_export]
-    use crate::ome::ChannelAcquisitionModeType;
-
-    #[pymodule_export]
-    use crate::ome::ChannelContrastMethodType;
-
-    #[pymodule_export]
-    use crate::ome::ChannelIlluminationType;
-
-    #[pymodule_export]
-    use crate::ome::DetectorType;
-
-    #[pymodule_export]
-    use crate::ome::ExperimentItemType;
-
-    #[pymodule_export]
-    use crate::ome::FilamentType;
-
-    #[pymodule_export]
-    use crate::ome::FilterType;
-
-    #[pymodule_export]
-    use crate::ome::FontFamilyType;
-
-    #[pymodule_export]
-    use crate::ome::LaserLaserMediumType;
-
-    #[pymodule_export]
-    use crate::ome::LaserPulseType;
-
-    #[pymodule_export]
-    use crate::ome::LaserType;
-
-    #[pymodule_export]
-    use crate::ome::LightSourceGroup;
-
-    #[pymodule_export]
-    use crate::ome::MarkerType;
-
-    #[pymodule_export]
-    use crate::ome::MicrobeamManipulationItemType;
-
-    #[pymodule_export]
-    use crate::ome::MicroscopeType;
-
-    #[pymodule_export]
-    use crate::ome::NamingConventionType;
-
-    #[pymodule_export]
-    use crate::ome::ObjectiveCorrectionType;
-
-    #[pymodule_export]
-    use crate::ome::ObjectiveImmersionType;
-
-    #[pymodule_export]
-    use crate::ome::ObjectiveSettingsMediumType;
-
-    #[pymodule_export]
-    use crate::ome::PixelType;
-
-    #[pymodule_export]
-    use crate::ome::PixelsDimensionOrderType;
-
-    #[pymodule_export]
-    use crate::ome::ShapeFillRuleType;
-
-    #[pymodule_export]
-    use crate::ome::ShapeFontStyleType;
-
-    #[pymodule_export]
-    use crate::ome::ShapeGroup;
-
-    #[pymodule_export]
-    use crate::ome::StructuredAnnotationsContent;
-
-    #[pymodule_export]
-    use crate::ome::UnitsElectricPotential;
-
-    #[pymodule_export]
-    use crate::ome::UnitsFrequency;
-
-    #[pymodule_export]
-    use crate::ome::UnitsLength;
-
-    #[pymodule_export]
-    use crate::ome::UnitsPower;
-
-    #[pymodule_export]
-    use crate::ome::UnitsPressure;
-
-    #[pymodule_export]
-    use crate::ome::UnitsTemperature;
-
-    #[pymodule_export]
-    use crate::ome::UnitsTime;
-
-    #[pymodule_init]
-    fn init(_: &Bound<'_, PyModule>) -> PyResult<()> {
-        let _ = color_eyre::install();
-        Ok(())
-    }
-}

ome-metadata/tests/1xp53-01-AP1.xml

@@ -1,416 +0,0 @@
-<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">
-  <Experimenter ID="Experimenter:0" UserName="r.hoogstraaten"/>
-  <Instrument ID="Instrument:0">
-    <Microscope Type="Inverted"/>
-    <Detector Model="" Offset="0.0" Zoom="1.7" ID="Detector:Airyscan" Type="Other"/>
-    <Detector Model="" ID="Detector:LSM980"/>
-    <Objective Model="C-Apochromat 40x/1.20 W autocorr UV VIS IR" ID="Objective:1" Immersion="Water" LensNA="1.2" NominalMagnification="40.0" WorkingDistance="280.0" WorkingDistanceUnit="µm"/>
-    <Dichroic ID="Dichroic:3"/>
-    <Dichroic ID="Dichroic:4"/>
-    <Dichroic ID="Dichroic:5"/>
-  </Instrument>
-  <Image ID="Image:0" Name="1xp53-01-AP1.czi #1">
-    <AcquisitionDate>2023-12-20T09:44:49.746</AcquisitionDate>
-    <ExperimenterRef ID="Experimenter:0"/>
-    <InstrumentRef ID="Instrument:0"/>
-    <ObjectiveSettings ID="Objective:1" Medium="Water" RefractiveIndex="1.33"/>
-    <StageLabel Name="Scene position #0" X="-2097.1" XUnit="µm" Y="-12106.7" YUnit="µm" Z="-2.96" ZUnit="µm"/>
-    <Pixels ID="Pixels:0" DimensionOrder="XYCZT" Type="uint16" SignificantBits="16" Interleaved="false" BigEndian="false" SizeX="1000" SizeY="1000" SizeZ="15" SizeC="1" SizeT="26" PhysicalSizeX="0.12185920266544126" PhysicalSizeXUnit="µm" PhysicalSizeY="0.12185920266544126" PhysicalSizeYUnit="µm" PhysicalSizeZ="0.5" PhysicalSizeZUnit="µm" TimeIncrement="19.92016" TimeIncrementUnit="s">
-      <Channel ID="Channel:0:0" Name="EGFP" SamplesPerPixel="1" IlluminationType="Epifluorescence" PinholeSize="215.8910436973" PinholeSizeUnit="µm" AcquisitionMode="LaserScanningConfocalMicroscopy" ExcitationWavelength="488.0" ExcitationWavelengthUnit="nm" EmissionWavelength="509.0" EmissionWavelengthUnit="nm" Fluor="EGFP" Color="16735231">
-        <DetectorSettings ID="Detector:Airyscan"/>
-        <LightPath/>
-      </Channel>
-      <MetadataOnly/>
-      <Plane TheZ="0" TheT="0" TheC="0" DeltaT="3.812999963760376" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="-2.96" PositionZUnit="µm"/>
-      <Plane TheZ="1" TheT="0" TheC="0" DeltaT="4.766000032424927" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="-2.46" PositionZUnit="µm"/>
-      <Plane TheZ="2" TheT="0" TheC="0" DeltaT="5.718999862670898" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="-1.96" PositionZUnit="µm"/>
-      <Plane TheZ="3" TheT="0" TheC="0" DeltaT="6.671999931335449" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="-1.46" PositionZUnit="µm"/>
-      <Plane TheZ="4" TheT="0" TheC="0" DeltaT="7.625" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="-0.96" PositionZUnit="µm"/>
-      <Plane TheZ="5" TheT="0" TheC="0" DeltaT="8.577999830245972" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="-0.46" PositionZUnit="µm"/>
-      <Plane TheZ="6" TheT="0" TheC="0" DeltaT="9.530999898910522" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="0.04" PositionZUnit="µm"/>
-      <Plane TheZ="7" TheT="0" TheC="0" DeltaT="10.483999967575073" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="0.54" PositionZUnit="µm"/>
-      <Plane TheZ="8" TheT="0" TheC="0" DeltaT="11.437000036239624" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="1.04" PositionZUnit="µm"/>
-      <Plane TheZ="9" TheT="0" TheC="0" DeltaT="12.389999866485596" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="1.54" PositionZUnit="µm"/>
-      <Plane TheZ="10" TheT="0" TheC="0" DeltaT="13.342999935150146" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="2.04" PositionZUnit="µm"/>
-      <Plane TheZ="11" TheT="0" TheC="0" DeltaT="14.294999837875366" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="2.54" PositionZUnit="µm"/>
-      <Plane TheZ="12" TheT="0" TheC="0" DeltaT="15.247999906539917" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="3.04" PositionZUnit="µm"/>
-      <Plane TheZ="13" TheT="0" TheC="0" DeltaT="16.200999975204468" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="3.54" PositionZUnit="µm"/>
-      <Plane TheZ="14" TheT="0" TheC="0" DeltaT="17.15400004386902" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="4.04" PositionZUnit="µm"/>
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ome-metadata/tests/4-Pos_001_002.xml

@@ -1,88 +0,0 @@
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-      <Plane TheZ="20" TheT="0" TheC="0" DeltaT="880258.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="4.15" PositionZUnit="µm"/>
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-  </Image>
-</OME>

ome-metadata/tests/Experiment-2029.xml

@@ -1,121 +0,0 @@
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-      <ExcitationFilterRef ID="Filter:5"/>
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-      <DichroicRef ID="Dichroic:1"/>
-      <EmissionFilterRef ID="Filter:2"/>
-      <EmissionFilterRef ID="Filter:4"/>
-      <EmissionFilterRef ID="Filter:6"/>
-      <EmissionFilterRef ID="Filter:8"/>
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-    <FilterSet ID="FilterSet:2">
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-    <Dichroic ID="Dichroic:2"/>
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-    <AcquisitionDate>2023-11-27T13:35:29.360</AcquisitionDate>
-    <ExperimenterRef ID="Experimenter:0"/>
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ome-metadata/tests/YTL1841B2-2-1_1hr_DMSO_galinduction_1.xml

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ome-metadata/tests/YTL1849A111_2023_05_04__14_46_19_cellnr_1_track.xml

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ome-metadata/tests/YTL378_JF552.xml

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ome-metadata/tests/beads_2023_05_04__19_00_22.xml

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-      <Plane TheZ="100" TheT="0" TheC="2" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.281" PositionZUnit="µm"/>
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-      <Plane TheZ="100" TheT="0" TheC="4" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.281" PositionZUnit="µm"/>
-      <Plane TheZ="100" TheT="0" TheC="5" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.281" PositionZUnit="µm"/>
-    </Pixels>
-  </Image>
-</OME>

ome-metadata/tests/multi-channel.ome.xml

@@ -1 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Creator="OME Bio-Formats 5.2.2" UUID="urn:uuid:bebd2be7-8253-4b90-be93-4df567ffe1be" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0" Name="multi-channel.ome.tif"><Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:0" Interleaved="false" SignificantBits="8" SizeC="3" SizeT="1" SizeX="439" SizeY="167" SizeZ="1" Type="int8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:1" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:2" SamplesPerPixel="1"><LightPath/></Channel><TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1"><UUID FileName="multi-channel.ome.tif">urn:uuid:bebd2be7-8253-4b90-be93-4df567ffe1be</UUID></TiffData><TiffData FirstC="1" FirstT="0" FirstZ="0" IFD="1" PlaneCount="1"><UUID FileName="multi-channel.ome.tif">urn:uuid:bebd2be7-8253-4b90-be93-4df567ffe1be</UUID></TiffData><TiffData FirstC="2" FirstT="0" FirstZ="0" IFD="2" PlaneCount="1"><UUID FileName="multi-channel.ome.tif">urn:uuid:bebd2be7-8253-4b90-be93-4df567ffe1be</UUID></TiffData></Pixels></Image></OME>

ome-metadata/tests/test.xml

@@ -1,12 +0,0 @@
-<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">
-  <Image ID="Image:0" Name="test.tif">
-    <AcquisitionDate>2025-01-29T14:42:42</AcquisitionDate>
-    <Description/>
-    <Pixels ID="Pixels:0" DimensionOrder="XYCZT" Type="int8" SignificantBits="8" Interleaved="false" BigEndian="false" SizeX="2" SizeY="2" SizeZ="1" SizeC="1" SizeT="1">
-      <Channel ID="Channel:0:0" SamplesPerPixel="1">
-        <LightPath/>
-      </Channel>
-      <MetadataOnly/>
-    </Pixels>
-  </Image>
-</OME>

parfor/__init__.py

@@ -0,0 +1,720 @@
+from __future__ import annotations
+
+import logging
+import os
+from collections import OrderedDict
+from contextlib import ExitStack, redirect_stderr, redirect_stdout
+from functools import wraps
+from importlib.metadata import version
+from io import StringIO
+from multiprocessing.shared_memory import SharedMemory
+from traceback import format_exc
+from typing import (
+    Any,
+    Callable,
+    Generator,
+    Hashable,
+    Iterable,
+    Iterator,
+    NoReturn,
+    Optional,
+    Protocol,
+    Sequence,
+    Sized,
+)
+
+import numpy as np
+import ray
+from numpy.typing import ArrayLike, DTypeLike
+from ray.remote_function import RemoteFunction
+from ray.types import ObjectRef
+from tqdm.auto import tqdm
+
+from .pickler import dumps, loads
+
+__version__ = version("parfor")
+cpu_count = int(os.cpu_count())
+
+
+class Bar(Protocol):
+    def update(self, n: int = 1) -> None: ...
+
+
+class SharedArray(np.ndarray):
+    """Numpy array whose memory can be shared between processes, so that memory use is reduced and changes in one
+    process are reflected in all other processes. Changes are not atomic, so protect changes with a lock to prevent
+    race conditions!
+    """
+
+    def __new__(
+        cls,
+        shape: int | Sequence[int],
+        dtype: DTypeLike = float,
+        shm: str | SharedMemory = None,
+        offset: int = 0,
+        strides: tuple[int, int] = None,
+        order: str = None,
+    ) -> SharedArray:
+        if isinstance(shm, str):
+            shm = SharedMemory(shm)
+        elif shm is None:
+            shm = SharedMemory(create=True, size=int(np.prod(shape) * np.dtype(dtype).itemsize))  # type: ignore
+        new = super().__new__(cls, shape, dtype, shm.buf, offset, strides, order)
+        new.shm = shm
+        return new  # type: ignore
+
+    def __reduce__(
+        self,
+    ) -> tuple[
+        Callable[[int | Sequence[int], DTypeLike, str], SharedArray],
+        tuple[int | tuple[int, ...], np.dtype, str],
+    ]:
+        return self.__class__, (self.shape, self.dtype, self.shm.name)
+
+    def __enter__(self) -> SharedArray:
+        return self
+
+    def __exit__(self, *args: Any, **kwargs: Any) -> None:
+        if hasattr(self, "shm"):
+            self.shm.close()
+            self.shm.unlink()
+
+    def __del__(self) -> None:
+        if hasattr(self, "shm"):
+            self.shm.close()
+
+    def __array_finalize__(self, obj: np.ndarray | None) -> None:
+        if isinstance(obj, np.ndarray) and not isinstance(obj, SharedArray):
+            raise TypeError("view casting to SharedArray is not implemented because right now we need to make a copy")
+
+    @classmethod
+    def from_array(cls, array: ArrayLike) -> SharedArray:
+        """copy existing array into a SharedArray"""
+        array = np.asarray(array)
+        new = cls(array.shape, array.dtype)
+        new[:] = array[:]
+        return new
+
+
+class Chunks(Iterable):
+    """Yield successive chunks from lists.
+    Usage: chunks(list0, list1, ...)
+           chunks(list0, list1, ..., size=s)
+           chunks(list0, list1, ..., number=n)
+           chunks(list0, list1, ..., ratio=r)
+    size:   size of chunks, might change to optimize division between chunks
+    number: number of chunks, coerced to 1 <= n <= len(list0)
+    ratio:  number of chunks / number of cpus, coerced to 1 <= n <= len(list0)
+    both size and number or ratio are given: use number or ratio, unless the chunk size would be bigger than size
+    both ratio and number are given: use ratio
+    """
+
+    def __init__(
+        self,
+        *iterables: Iterable[Any] | Sized,
+        size: int = None,
+        number: int = None,
+        ratio: float = None,
+        length: int = None,
+    ) -> None:
+        if length is None:
+            try:
+                length = min(*[len(iterable) for iterable in iterables]) if len(iterables) > 1 else len(iterables[0])
+            except TypeError:
+                raise TypeError(
+                    "Cannot determine the length of the iterables(s), so the length must be provided as an argument."
+                )
+        if size is not None and (number is not None or ratio is not None):
+            if number is None:
+                number = int(cpu_count * ratio)
+            if length >= size * number:
+                number = round(length / size)
+        elif size is not None:  # size of chunks
+            number = round(length / size)
+        elif ratio is not None:  # number of chunks
+            number = int(cpu_count * ratio)
+        self.iterators = [iter(arg) for arg in iterables]
+        self.number_of_items = length
+        self.length = min(length, number)
+        self.lengths = [
+            ((i + 1) * self.number_of_items // self.length) - (i * self.number_of_items // self.length)
+            for i in range(self.length)
+        ]
+
+    def __iter__(self) -> Iterator[Any]:
+        for i in range(self.length):
+            p, q = (
+                (i * self.number_of_items // self.length),
+                ((i + 1) * self.number_of_items // self.length),
+            )
+            if len(self.iterators) == 1:
+                yield [next(self.iterators[0]) for _ in range(q - p)]
+            else:
+                yield [[next(iterator) for _ in range(q - p)] for iterator in self.iterators]
+
+    def __len__(self) -> int:
+        return self.length
+
+
+class ExternalBar(Iterable):
+    def __init__(
+        self,
+        iterable: Iterable = None,
+        callback: Callable[[int], None] = None,
+        total: int = 0,
+    ) -> None:
+        self.iterable = iterable
+        self.callback = callback
+        self.total = total
+        self._n = 0
+
+    def __enter__(self) -> ExternalBar:
+        return self
+
+    def __exit__(self, *args: Any, **kwargs: Any) -> None:
+        return
+
+    def __iter__(self) -> Iterator[Any]:
+        for n, item in enumerate(self.iterable):
+            yield item
+            self.n = n + 1
+
+    def update(self, n: int = 1) -> None:
+        self.n += n
+
+    @property
+    def n(self) -> int:
+        return self._n
+
+    @n.setter
+    def n(self, n: int) -> None:
+        if n != self._n:
+            self._n = n
+            if self.callback is not None:
+                self.callback(n)
+
+
+def get_worker(n_processes) -> RemoteFunction:
+    n_processes = n_processes or PoolSingleton.cpu_count
+    num_cpus = None if n_processes is None else cpu_count / n_processes
+
+    if not ray.is_initialized():
+        os.environ["RAY_ACCEL_ENV_VAR_OVERRIDE_ON_ZERO"] = "0"
+        ray.init(logging_level=logging.ERROR, log_to_driver=False, include_dashboard=False)
+
+    def worker(task):
+        try:
+            with ExitStack() as stack:  # noqa
+                if task.allow_output:
+                    out = StringIO()
+                    err = StringIO()
+                    stack.enter_context(redirect_stdout(out))
+                    stack.enter_context(redirect_stderr(err))
+                else:
+                    stack.enter_context(redirect_stdout(open(os.devnull, "w")))
+                    stack.enter_context(redirect_stderr(open(os.devnull, "w")))
+                try:
+                    task()
+                    task.status = ("done",)
+                except Exception:  # noqa
+                    task.status = "task_error", format_exc()
+                if task.allow_output:
+                    task.out = out.getvalue()
+                    task.err = err.getvalue()
+        except KeyboardInterrupt:  # noqa
+            pass
+
+        return task
+
+    if num_cpus:
+        return ray.remote(num_cpus=num_cpus)(worker)  # type: ignore
+    else:
+        return ray.remote(worker)  # type: ignore
+
+
+class DequeDict(OrderedDict):
+    def __init__(self, maxlen: int = None, *args: Any, **kwargs: Any) -> None:
+        self.maxlen = maxlen
+        super().__init__(*args, **kwargs)
+
+    def __setitem__(self, *args: Any, **kwargs: Any) -> None:
+        super().__setitem__(*args, **kwargs)
+        self.truncate()
+
+    def truncate(self) -> None:
+        if self.maxlen is not None:
+            while len(self) > self.maxlen:
+                self.popitem(False)
+
+    def update(self, *args: Any, **kwargs: Any) -> None:
+        super().update(*args, **kwargs)  # type: ignore
+        self.truncate()
+
+
+cache = DequeDict(128)
+
+
+class Task:
+    def __init__(
+        self,
+        handle: Hashable,
+        fun: Callable[[Any, ...], Any],
+        args: tuple[Any, ...] = (),
+        kwargs: dict[str, Any] = None,
+        allow_output: bool = False,
+    ) -> None:
+        self.handle = handle
+        self.fun = fun
+        self.args = args
+        self.kwargs = kwargs or {}
+        self.name = fun.__name__ if hasattr(fun, "__name__") else None
+        self.done = False
+        self.result = None
+        self.out = None
+        self.err = None
+        self.future = None
+        self.status = "starting"
+        self.allow_output = allow_output
+
+    @staticmethod
+    def get(item: tuple[bool, Any]) -> Any:
+        if item[0]:
+            return loads(ray.get(item[1]))
+        else:
+            return ray.get(item[1])
+
+    @staticmethod
+    def put(item: Any) -> tuple[bool, Any]:
+        try:
+            h = hash(item)
+            if not h in cache:
+                try:
+                    cache[h] = False, ray.put(item)
+                except Exception:  # noqa
+                    cache[h] = True, ray.put(dumps(item, recurse=True))
+            else:
+                cache.move_to_end(h)
+            return cache[h]
+        except TypeError:
+            try:
+                return False, ray.put(item)
+            except Exception:  # noqa
+                return True, ray.put(dumps(item, recurse=True))
+
+    @property
+    def fun(self) -> Callable[[Any, ...], Any]:
+        return self.get(self._fun)
+
+    @fun.setter
+    def fun(self, fun: Callable[[Any, ...], Any]):
+        self._fun = self.put(fun)
+
+    @property
+    def args(self) -> tuple[Any, ...]:
+        return tuple([self.get(arg) for arg in self._args])
+
+    @args.setter
+    def args(self, args: tuple[Any, ...]) -> None:
+        self._args = [self.put(arg) for arg in args]
+
+    @property
+    def kwargs(self) -> dict[str, Any]:
+        return {key: self.get(value) for key, value in self._kwargs.items()}
+
+    @kwargs.setter
+    def kwargs(self, kwargs: dict[str, Any]) -> None:
+        self._kwargs = {key: self.put(value) for key, value in kwargs.items()}
+
+    @property
+    def result(self) -> Any:
+        return self.get(self._result)
+
+    @result.setter
+    def result(self, result: Any) -> None:
+        self._result = self.put(result)
+
+    def __call__(self) -> Task:
+        if not self.done:
+            self.result = self.fun(*self.args, **self.kwargs)  # noqa
+            self.done = True
+        return self
+
+    def __repr__(self) -> str:
+        if self.done:
+            return f"Task {self.handle}, result: {self.result}"
+        else:
+            return f"Task {self.handle}"
+
+
+class ParPool:
+    """Parallel processing with addition of iterations at any time and request of that result any time after that.
+    The target function and its argument can be changed at any time.
+    """
+
+    def __init__(
+        self,
+        fun: Callable[[Any, ...], Any] = None,
+        args: tuple[Any] = None,
+        kwargs: dict[str, Any] = None,
+        n_processes: int = None,
+        bar: Bar = None,
+        allow_output: bool = False,
+    ):
+        self.handle = 0
+        self.tasks = {}
+        self.bar = bar
+        self.bar_lengths = {}
+        self.allow_output = allow_output
+        self.fun = fun
+        self.args = args
+        self.kwargs = kwargs
+        self.n_processes = n_processes or PoolSingleton.cpu_count
+        self.worker = get_worker(self.n_processes)
+
+    def __getstate__(self) -> NoReturn:
+        raise RuntimeError(f"Cannot pickle {self.__class__.__name__} object.")
+
+    def __enter__(self) -> ParPool:
+        return self
+
+    def __exit__(self, *args: Any, **kwargs: Any) -> None:
+        self.close()
+
+    def __call__(self, n: Any, handle: Hashable = None, barlength: int = 1) -> None:
+        self.add_task(
+            args=(n, *(() if self.args is None else self.args)),
+            handle=handle,
+            barlength=barlength,
+        )
+
+    def close(self) -> None:
+        cache.clear()
+
+    def add_task(
+        self,
+        fun: Callable[[Any, ...], Any] = None,
+        args: tuple[Any, ...] = None,
+        kwargs: dict[str, Any] = None,
+        handle: Hashable = None,
+        barlength: int = 1,
+        allow_output: bool = False,
+    ) -> Optional[int]:
+        if handle is None:
+            new_handle = self.handle
+            self.handle += 1
+        else:
+            new_handle = handle
+        if new_handle in self:
+            raise ValueError(f"handle {new_handle} already present")
+        task = Task(
+            new_handle,
+            fun or self.fun,
+            args or self.args,
+            kwargs or self.kwargs,
+            allow_output or self.allow_output,
+        )
+        self.block_until_space_available()
+        task.future = self.worker.remote(task)
+        self.tasks[new_handle] = task
+        self.bar_lengths[new_handle] = barlength
+        if handle is None:
+            return new_handle
+        else:
+            return None
+
+    def __setitem__(self, handle: Hashable, n: Any) -> None:
+        """Add new iteration."""
+        self(n, handle=handle)
+
+    def __getitem__(self, handle: Hashable) -> Any:
+        """Request result and delete its record. Wait if result not yet available."""
+        if handle not in self:
+            raise KeyError(f"No task with handle: {handle} in pool")
+        task = self.finalize_task(self.tasks[handle])
+        self.tasks.pop(task.handle)
+        return task.result
+
+    def __contains__(self, handle: Hashable) -> bool:
+        return handle in self.tasks
+
+    def __delitem__(self, handle: Hashable) -> None:
+        self.tasks.pop(handle)
+
+    def finalize_task(self, future: ObjectRef | Task) -> Task:
+        if isinstance(future, Task):
+            task: Task = future
+            future = task.future
+        else:
+            task = None  # type: ignore
+
+        if future is not None:
+            task: Task = ray.get(future)  # type: ignore
+            code, *args = task.status
+            if task.out:
+                if hasattr(self.bar, "write"):
+                    self.bar.write(task.out, end="")
+                else:
+                    print(task.out, end="")
+            if task.err:
+                if hasattr(self.bar, "write"):
+                    self.bar.write(task.err, end="")
+                else:
+                    print(task.err, end="")
+            getattr(self, code)(task, *args)
+            self.tasks[task.handle] = task
+        return task
+
+    def block_until_space_available(self) -> None:
+        if len(self.tasks) < 3 * self.n_processes:
+            return
+        while True:
+            if self.tasks:
+                futures = [task.future for task in self.tasks.values() if task.future is not None]
+                done, busy = ray.wait(futures, num_returns=1, timeout=0.01)
+                for d in done:
+                    self.finalize_task(d)  # type: ignore
+                if len(busy) < 3 * self.n_processes:
+                    return
+
+    def get_newest(self) -> Any:
+        """Request the newest handle and result and delete its record. Wait if result not yet available."""
+        if self.tasks:
+            done = [task for task in self.tasks.values() if task.future is None]
+            if done:
+                task = done[0]
+                self.tasks.pop(task.handle)
+                return task.handle, task.result
+            while True:
+                futures = [task.future for task in self.tasks.values() if task.future is not None]
+                done, _ = ray.wait(futures, num_returns=1, timeout=0.01)
+                if done:
+                    task = self.finalize_task(done[0])
+                    self.tasks.pop(task.handle)
+                    return task.handle, task.result
+        raise StopIteration
+
+    def task_error(self, task: Task, error: Exception) -> None:
+        if task.handle in self:
+            task = self.tasks[task.handle]
+            print(f"Error from process working on iteration {task.handle}:\n")
+            print(error)
+            print("Retrying in main process...")
+            task()
+            raise Exception(f"Function '{task.name}' cannot be executed by parfor, amend or execute in serial.")
+
+    def done(self, task: Task) -> None:
+        if task.handle in self:  # if not, the task was restarted erroneously
+            self.tasks[task.handle] = task
+            if hasattr(self.bar, "update"):
+                self.bar.update(self.bar_lengths.pop(task.handle))
+
+
+class PoolSingleton:
+    cpu_count: int = os.cpu_count()
+
+    @staticmethod
+    def close(*args, **kwargs) -> None:
+        pass
+
+
+class Worker:
+    nested: bool = False
+
+
+def gmap(
+    fun: Callable[[Any, ...], Any],
+    iterable: Iterable[Any] = None,
+    args: tuple[Any, ...] = None,
+    kwargs: dict[str, Any] = None,
+    total: int = None,
+    desc: str = None,
+    bar: Bar | bool = True,
+    serial: bool = None,
+    n_processes: int = None,
+    yield_ordered: bool = True,
+    yield_index: bool = False,
+    allow_output: bool = False,
+    **bar_kwargs: Any,
+) -> Generator[Any, None, None]:
+    """map a function fun to each iteration in iterable
+    use as a function: pmap
+    use as a decorator: parfor
+    best use: iterable is a generator and length is given to this function as 'total'
+
+    required:
+        fun:    function taking arguments: iteration from  iterable, other arguments defined in args & kwargs
+        iterable: iterable or iterator from which an item is given to fun as a first argument
+    optional:
+        args:   tuple with other unnamed arguments to fun
+        kwargs: dict with other named arguments to fun
+        total:  give the length of the iterator in cases where len(iterator) results in an error
+        desc:   string with description of the progress bar
+        bar:    bool enable progress bar,
+                    or a callback function taking the number of passed iterations as an argument
+        serial: execute in series instead of parallel if True, None (default): let pmap decide
+        n_processes: number of processes to use,
+            the parallel pool will be restarted if the current pool does not have the right number of processes
+        yield_ordered: return the result in the same order as the iterable
+        yield_index: return the index of the result too
+        allow_output: allow output from subprocesses
+        **bar_kwargs: keywords arguments for tqdm.tqdm
+
+    output:
+        list (pmap) or generator (gmap) with results from applying the function \'fun\' to each iteration
+         of the iterable / iterator
+
+    examples:
+        << from time import sleep
+        <<
+        @parfor(range(10), (3,))
+        def fun(i, a):
+            sleep(1)
+            return a * i ** 2
+        fun
+        >> [0, 3, 12, 27, 48, 75, 108, 147, 192, 243]
+
+        <<
+        def fun(i, a):
+            sleep(1)
+            return a * i ** 2
+        pmap(fun, range(10), (3,))
+        >> [0, 3, 12, 27, 48, 75, 108, 147, 192, 243]
+
+        equivalent to using the deco module:
+        <<
+        @concurrent
+        def fun(i, a):
+            time.sleep(1)
+            return a * i ** 2
+
+        @synchronized
+        def run(iterator, a):
+            res = []
+            for i in iterator:
+                res.append(fun(i, a))
+            return res
+        run(range(10), 3)
+        >> [0, 3, 12, 27, 48, 75, 108, 147, 192, 243]
+
+        all equivalent to the serial for-loop:
+        <<
+        a = 3
+        fun = []
+        for i in range(10):
+            sleep(1)
+            fun.append(a * i ** 2)
+        fun
+        >> [0, 3, 12, 27, 48, 75, 108, 147, 192, 243]
+    """
+    is_chunked = isinstance(iterable, Chunks)
+    if is_chunked:
+        chunk_fun = fun
+    else:
+        iterable = Chunks(iterable, ratio=5, length=total)
+
+        @wraps(fun)
+        def chunk_fun(iterable: Iterable, *args: Any, **kwargs: Any) -> list[Any]:  # noqa
+            return [fun(iteration, *args, **kwargs) for iteration in iterable]
+
+    if args is None:
+        args = ()
+    if kwargs is None:
+        kwargs = {}
+
+    if "total" not in bar_kwargs:
+        bar_kwargs["total"] = sum(iterable.lengths)
+    if "desc" not in bar_kwargs:
+        bar_kwargs["desc"] = desc
+    if "disable" not in bar_kwargs:
+        bar_kwargs["disable"] = not bar
+    if serial is True or (serial is None and len(iterable) < min(cpu_count, 4)):  # serial case
+
+        def tqdm_chunks(chunks: Chunks, *args, **kwargs) -> Iterable[Any]:  # noqa
+            with tqdm(*args, **kwargs) as b:
+                for chunk, length in zip(chunks, chunks.lengths):  # noqa
+                    yield chunk
+                    b.update(length)
+
+        iterable = (
+            ExternalBar(iterable, bar, sum(iterable.lengths)) if callable(bar) else tqdm_chunks(iterable, **bar_kwargs)  # type: ignore
+        )
+        if is_chunked:
+            if yield_index:
+                for i, c in enumerate(iterable):
+                    yield i, chunk_fun(c, *args, **kwargs)
+            else:
+                for c in iterable:
+                    yield chunk_fun(c, *args, **kwargs)
+        else:
+            if yield_index:
+                for i, c in enumerate(iterable):
+                    for q in chunk_fun(c, *args, **kwargs):
+                        yield i, q
+            else:
+                for c in iterable:
+                    yield from chunk_fun(c, *args, **kwargs)
+
+    else:  # parallel case
+        with ExitStack() as stack:  # noqa
+            if callable(bar):
+                bar = stack.enter_context(ExternalBar(callback=bar))  # noqa
+            else:
+                bar = stack.enter_context(tqdm(**bar_kwargs))
+            with ParPool(chunk_fun, args, kwargs, n_processes, bar, allow_output) as p:  # type: ignore
+                for i, (j, l) in enumerate(zip(iterable, iterable.lengths)):  # add work to the queue
+                    p(j, handle=i, barlength=l)
+                    if bar.total is None or bar.total < i + 1:
+                        bar.total = i + 1
+
+                if is_chunked:
+                    if yield_ordered:
+                        if yield_index:
+                            for i in range(len(iterable)):
+                                yield i, p[i]
+                        else:
+                            for i in range(len(iterable)):
+                                yield p[i]
+                    else:
+                        if yield_index:
+                            for _ in range(len(iterable)):
+                                yield p.get_newest()
+                        else:
+                            for _ in range(len(iterable)):
+                                yield p.get_newest()[1]
+                else:
+                    if yield_ordered:
+                        if yield_index:
+                            for i in range(len(iterable)):
+                                for q in p[i]:
+                                    yield i, q
+                        else:
+                            for i in range(len(iterable)):
+                                yield from p[i]
+                    else:
+                        if yield_index:
+                            for _ in range(len(iterable)):
+                                i, n = p.get_newest()
+                                for q in n:
+                                    yield i, q
+                        else:
+                            for _ in range(len(iterable)):
+                                yield from p.get_newest()[1]
+
+
+def pmap(*args, **kwargs) -> list[Any]:
+    return list(gmap(*args, **kwargs))
+
+
+def parfor(*args: Any, **kwargs: Any) -> Callable[[Callable[[Any, ...], Any]], list[Any]]:
+    def decfun(fun: Callable[[Any, ...], Any]) -> list[Any]:
+        return pmap(fun, *args, **kwargs)
+
+    return decfun
+
+
+try:
+    parfor.__doc__ = pmap.__doc__ = gmap.__doc__
+    pmap.__annotations__ = gmap.__annotations__ | pmap.__annotations__
+    parfor.__annotations__ = {key: value for key, value in pmap.__annotations__.items() if key != "fun"}
+except AttributeError:
+    pass

parfor/pickler.py

@@ -0,0 +1,119 @@
+from __future__ import annotations
+
+import copyreg
+from io import BytesIO
+from pickle import PicklingError
+from typing import Any, Callable
+
+import dill
+
+loads = dill.loads
+
+
+class CouldNotBePickled:
+    def __init__(self, class_name: str) -> None:
+        self.class_name = class_name
+
+    def __repr__(self) -> str:
+        return f"Item of type '{self.class_name}' could not be pickled and was omitted."
+
+    @classmethod
+    def reduce(cls, item: Any) -> tuple[Callable[[str], CouldNotBePickled], tuple[str]]:
+        return cls, (type(item).__name__,)
+
+
+class Pickler(dill.Pickler):
+    """Overload dill to ignore unpicklable parts of objects.
+    You probably didn't want to use these parts anyhow.
+    However, if you did, you'll have to find some way to make them picklable.
+    """
+
+    def save(self, obj: Any, save_persistent_id: bool = True) -> None:
+        """Copied from pickle and amended."""
+        self.framer.commit_frame()
+
+        # Check for persistent id (defined by a subclass)
+        pid = self.persistent_id(obj)
+        if pid is not None and save_persistent_id:
+            self.save_pers(pid)
+            return
+
+        # Check the memo
+        x = self.memo.get(id(obj))
+        if x is not None:
+            self.write(self.get(x[0]))
+            return
+
+        rv = NotImplemented
+        reduce = getattr(self, "reducer_override", None)
+        if reduce is not None:
+            rv = reduce(obj)
+
+        if rv is NotImplemented:
+            # Check the type dispatch table
+            t = type(obj)
+            f = self.dispatch.get(t)
+            if f is not None:
+                f(self, obj)  # Call unbound method with explicit self
+                return
+
+            # Check private dispatch table if any, or else
+            # copyreg.dispatch_table
+            reduce = getattr(self, "dispatch_table", copyreg.dispatch_table).get(t)
+            if reduce is not None:
+                rv = reduce(obj)
+            else:
+                # Check for a class with a custom metaclass; treat as regular
+                # class
+                if issubclass(t, type):
+                    self.save_global(obj)
+                    return
+
+                # Check for a __reduce_ex__ method, fall back to __reduce__
+                reduce = getattr(obj, "__reduce_ex__", None)
+                try:
+                    if reduce is not None:
+                        rv = reduce(self.proto)
+                    else:
+                        reduce = getattr(obj, "__reduce__", None)
+                        if reduce is not None:
+                            rv = reduce()
+                        else:
+                            raise PicklingError("Can't pickle %r object: %r" % (t.__name__, obj))
+                except Exception:  # noqa
+                    rv = CouldNotBePickled.reduce(obj)
+
+        # Check for string returned by reduce(), meaning "save as global"
+        if isinstance(rv, str):
+            try:
+                self.save_global(obj, rv)
+            except Exception:  # noqa
+                self.save_global(obj, CouldNotBePickled.reduce(obj))
+            return
+
+        # Assert that reduce() returned a tuple
+        if not isinstance(rv, tuple):
+            raise PicklingError("%s must return string or tuple" % reduce)
+
+        # Assert that it returned an appropriately sized tuple
+        length = len(rv)
+        if not (2 <= length <= 6):
+            raise PicklingError("Tuple returned by %s must have two to six elements" % reduce)
+
+        # Save the reduce() output and finally memoize the object
+        try:
+            self.save_reduce(obj=obj, *rv)
+        except Exception:  # noqa
+            self.save_reduce(obj=obj, *CouldNotBePickled.reduce(obj))
+
+
+def dumps(
+    obj: Any, protocol: str = None, byref: bool = None, fmode: str = None, recurse: bool = True, **kwds: Any
+) -> bytes:
+    """pickle an object to a string"""
+    protocol = dill.settings["protocol"] if protocol is None else int(protocol)
+    _kwds = kwds.copy()
+    _kwds.update(dict(byref=byref, fmode=fmode, recurse=recurse))
+    with BytesIO() as file:
+        Pickler(file, protocol, **_kwds).dump(obj)
+        return file.getvalue()

pyproject.toml

@@ -0,0 +1,30 @@
+[project]
+name = "parfor"
+version = "2026.5.0"
+description = "A package to mimic the use of parfor as done in Matlab."
+authors = [
+    { name = "Wim Pomp-Pervova", email = "wimpomp@gmail.com" }
+]
+license = { text = "MIT" }
+readme = "README.md"
+keywords = ["parfor", "concurrency", "multiprocessing", "parallel"]
+requires-python = ">=3.10"
+dependencies = [
+    "dill >= 0.3.0",
+    "numpy",
+    "tqdm >= 4.50.0",
+    "ray",
+]
+
+[project.urls]
+repository = "https://git.wimpomp.nl/wim/parfor"
+
+[project.optional-dependencies]
+test = ["pytest"]
+
+[tool.ruff]
+line-length = 119
+indent-width = 4
+
+[tool.isort]
+line_length = 119

tests/test_parfor.py

@@ -0,0 +1,174 @@
+from __future__ import annotations
+
+from dataclasses import dataclass
+from os import getpid
+from time import sleep
+from typing import Any, Iterator, Optional, Sequence
+
+import numpy as np
+import pytest
+
+from parfor import Chunks, ParPool, SharedArray, parfor, pmap
+
+
+class SequenceIterator:
+    def __init__(self, sequence: Sequence) -> None:
+        self._sequence = sequence
+        self._index = 0
+
+    def __iter__(self) -> SequenceIterator:
+        return self
+
+    def __next__(self) -> Any:
+        if self._index < len(self._sequence):
+            item = self._sequence[self._index]
+            self._index += 1
+            return item
+        else:
+            raise StopIteration
+
+    def __len__(self) -> int:
+        return len(self._sequence)
+
+
+class Iterable:
+    def __init__(self, sequence: Sequence) -> None:
+        self.sequence = sequence
+
+    def __iter__(self) -> SequenceIterator:
+        return SequenceIterator(self.sequence)
+
+
+def iterators() -> tuple[Iterator, Optional[int]]:
+    yield range(10), None
+    yield list(range(10)), None
+    yield (i for i in range(10)), 10
+    yield SequenceIterator(range(10)), None
+    yield Iterable(range(10)), 10
+
+
+@pytest.mark.parametrize("iterator", iterators())
+def test_chunks(iterator: tuple[Iterator, Optional[int]]) -> None:
+    chunks = Chunks(iterator[0], size=2, length=iterator[1])
+    assert list(chunks) == [[0, 1], [2, 3], [4, 5], [6, 7], [8, 9]]
+
+
+def test_parpool() -> None:
+    def fun(i, j, k) -> int:  # noqa
+        return i * j * k
+
+    with ParPool(fun, (3,), {"k": 2}) as pool:  # noqa
+        for i in range(10):
+            pool[i] = i
+
+        assert [pool[i] for i in range(10)] == [0, 6, 12, 18, 24, 30, 36, 42, 48, 54]
+
+
+def test_parfor() -> None:
+    @parfor(range(10), (3,), {"k": 2})
+    def fun(i, j, k):
+        return i * j * k
+
+    assert fun == [0, 6, 12, 18, 24, 30, 36, 42, 48, 54]
+
+
+@pytest.mark.parametrize("serial", (True, False))
+def test_pmap(serial) -> None:
+    def fun(i, j, k):
+        return i * j * k
+
+    assert pmap(fun, range(10), (3,), {"k": 2}, serial=serial) == [
+        0,
+        6,
+        12,
+        18,
+        24,
+        30,
+        36,
+        42,
+        48,
+        54,
+    ]
+
+
+@pytest.mark.parametrize("serial", (True, False))
+def test_pmap_with_idx(serial) -> None:
+    def fun(i, j, k):
+        return i * j * k
+
+    assert pmap(fun, range(10), (3,), {"k": 2}, serial=serial, yield_index=True) == [
+        (0, 0),
+        (1, 6),
+        (2, 12),
+        (3, 18),
+        (4, 24),
+        (5, 30),
+        (6, 36),
+        (7, 42),
+        (8, 48),
+        (9, 54),
+    ]
+
+
+@pytest.mark.parametrize("serial", (True, False))
+def test_pmap_chunks(serial) -> None:
+    def fun(i, j, k):
+        return [i_ * j * k for i_ in i]
+
+    chunks = Chunks(range(10), size=2)
+    assert pmap(fun, chunks, (3,), {"k": 2}, serial=serial) == [
+        [0, 6],
+        [12, 18],
+        [24, 30],
+        [36, 42],
+        [48, 54],
+    ]
+
+
+def test_id_reuse() -> None:
+    def fun(i):
+        return i[0].a
+
+    @dataclass
+    class T:
+        a: int = 3
+
+    def gen(total):
+        for i in range(total):
+            t = T(i)
+            yield t
+            del t
+
+    a = pmap(fun, Chunks(gen(1000), size=1, length=1000), total=1000)  # noqa
+    assert all([i == j for i, j in enumerate(a)])
+
+
+@pytest.mark.parametrize("n_processes", (2, 4, 6))
+def test_n_processes(n_processes) -> None:
+    @parfor(range(12), n_processes=n_processes)
+    def fun(i):  # noqa
+        sleep(0.25)
+        return getpid()
+
+    assert len(set(fun)) <= n_processes
+
+
+def test_shared_array() -> None:
+    def fun(i, a):
+        a[i] = i
+
+    with SharedArray(100, int) as arr:
+        pmap(fun, range(len(arr)), (arr,))
+        b = np.array(arr)
+
+    assert np.all(b == np.arange(len(arr)))
+
+
+def test_nesting() -> None:
+    def a(i):
+        return i**2
+
+    def b(i):
+        return pmap(a, range(i, i + 50))
+
+    assert pmap(b, range(10)) == [[i**2 for i in range(j, j + 50)] for j in range(10)]