diff --git a/.github/actions/dependencies/action.yml b/.github/actions/dependencies/action.yml new file mode 100644 index 00000000..69e80abe --- /dev/null +++ b/.github/actions/dependencies/action.yml @@ -0,0 +1,12 @@ +name: PDM & Dependencies +description: Install PDM and dependencies +runs: + using: composite + steps: + - uses: ./.github/actions/pdm + + - name: Install dependencies + shell: bash + # --only-keep flag in case the environment is restored from a stale cache. + run: | + pdm sync -d --only-keep \ No newline at end of file diff --git a/.github/actions/pdm/action.yml b/.github/actions/pdm/action.yml new file mode 100644 index 00000000..e4f76755 --- /dev/null +++ b/.github/actions/pdm/action.yml @@ -0,0 +1,11 @@ +name: PDM +description: Install PDM +runs: + using: composite + steps: + - name: Set up PDM + uses: pdm-project/setup-pdm@v4 + with: + python-version: "3.9" + # Cache all dependencies installed from pdm.lock + cache: true \ No newline at end of file diff --git a/.github/workflows/analyze.yml b/.github/workflows/analyze.yml index 60c31eb0..cda81e81 100644 --- a/.github/workflows/analyze.yml +++ b/.github/workflows/analyze.yml @@ -16,27 +16,18 @@ jobs: os: [ubuntu-latest] steps: - uses: actions/checkout@v4.2.2 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - cache: "pip" - cache-dependency-path: setup.py - - name: Install Dependencies - run: | - python -m pip install --upgrade pip - pip install .[all] + - uses: ./.github/actions/dependencies - name: Pack test recipe run: | - pack -r cellpack/tests/recipes/v2/test_spheres.json -c cellpack/tests/packing-configs/test_config.json + pdm run pack -r cellpack/tests/recipes/v2/test_spheres.json -c cellpack/tests/packing-configs/test_config.json - name: Modify JSON with PR sub_directory path run: | jq --arg branch_name "${{ github.ref_name }}" '.create_report.output_image_location |= "https://cellpack-results.s3.us-west-2.amazonaws.com/\($branch_name)/spheresSST/figures"' cellpack/tests/analysis-configs/PR_analysis_config.json > cellpack/tests/analysis-configs/PR_analysis_config_temp.json mv cellpack/tests/analysis-configs/PR_analysis_config_temp.json cellpack/tests/analysis-configs/PR_analysis_config.json - name: Run analysis code - run: analyze -r cellpack/tests/recipes/v2/test_spheres.json -a cellpack/tests/analysis-configs/PR_analysis_config.json -p cellpack/tests/outputs/test_spheres/spheresSST + run: pdm run analyze -r cellpack/tests/recipes/v2/test_spheres.json -a cellpack/tests/analysis-configs/PR_analysis_config.json -p cellpack/tests/outputs/test_spheres/spheresSST - name: Upload results - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: results path: cellpack/tests/outputs/test_spheres/ @@ -59,10 +50,10 @@ jobs: aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }} aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }} aws-region: us-west-2 - - uses: actions/download-artifact@v3 + - uses: actions/download-artifact@v4 - name: Copy files to results bucket run: aws s3 cp ./results s3://cellpack-results/${{ github.ref_name }}/ --recursive --acl public-read - - uses: iterative/setup-cml@v1 + - uses: iterative/setup-cml@v2 - name: Update comment for dependabot if: ${{ github.actor == 'dependabot[bot]' }} env: diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml index ff5b2c73..460b4357 100644 --- a/.github/workflows/build-docs.yml +++ b/.github/workflows/build-docs.yml @@ -13,16 +13,7 @@ jobs: - uses: actions/checkout@v4.2.2 with: persist-credentials: false - - name: Set up Python - uses: actions/setup-python@v5 - with: - python-version: 3.9 - cache: "pip" - cache-dependency-path: setup.py - - name: Install Dependencies - run: | - pip install --upgrade pip - pip install .[dev] + - uses: ./.github/actions/dependencies - name: Generate Docs run: | make gen-docs diff --git a/.github/workflows/cache-dependencies.yml b/.github/workflows/cache-dependencies.yml new file mode 100644 index 00000000..548d2955 --- /dev/null +++ b/.github/workflows/cache-dependencies.yml @@ -0,0 +1,18 @@ +# The purpose of this workflow is to get more cache hits when other workflows build dependencies. +# Github actions do not share caches between branches, except that all branches can pull results +# from the default (main) branch. Therefore, this workflow runs on the main branch to keep the +# latest dependencies cached for other branches to use. +# Branches that change the dependencies will still get cache misses. +name: Build and cache dependencies on main + +on: + push: + branches: + - main + +jobs: + dependencies: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: ./.github/actions/dependencies \ No newline at end of file diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 7730ca10..0616a5b4 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -31,19 +31,10 @@ jobs: steps: - uses: actions/checkout@v4.2.2 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - cache: "pip" - cache-dependency-path: setup.py - - name: Install Dependencies - run: | - python -m pip install --upgrade pip - pip install .[all] + - uses: ./.github/actions/dependencies - name: Test with pytest run: | - pytest --cov cellpack/tests/ + pdm run pytest --cov cellpack/tests/ - name: Upload codecov uses: codecov/codecov-action@v4 @@ -52,22 +43,13 @@ jobs: if: ${{ !contains(github.event.head_commit.message, 'Bump version') }} steps: - uses: actions/checkout@v4.2.2 - - name: Set up Python - uses: actions/setup-python@v5 - with: - python-version: 3.9 - cache: "pip" - cache-dependency-path: setup.py - - name: Install Dependencies - run: | - python -m pip install --upgrade pip - pip install .[test] + - uses: ./.github/actions/dependencies - name: Lint with flake8 run: | - flake8 cellpack --count --verbose --show-source --statistics --ignore=E501,E277,W503,E203 + pdm run flake8 cellpack --count --verbose --show-source --statistics --ignore=E501,E277,W503,E203 - name: Check with black run: | - black --check cellpack + pdm run black --check cellpack publish: if: success() && startsWith(github.ref, 'refs/tags/') @@ -81,19 +63,7 @@ jobs: steps: - uses: actions/checkout@v4.2.2 - - name: Set up Python - uses: actions/setup-python@v5 - with: - python-version: 3.9 - cache: "pip" - cache-dependency-path: setup.py - - name: Install Dependencies - run: | - python -m pip install --upgrade pip - pip install setuptools wheel - - name: Build Package - run: | - python setup.py sdist bdist_wheel + - uses: ./.github/actions/dependencies - name: Publish to PyPI - uses: pypa/gh-action-pypi-publish@release/v1 + run: pdm publish diff --git a/.github/workflows/cleanup.yml b/.github/workflows/cleanup-aws.yml similarity index 96% rename from .github/workflows/cleanup.yml rename to .github/workflows/cleanup-aws.yml index 45428f5b..b4fff1b6 100644 --- a/.github/workflows/cleanup.yml +++ b/.github/workflows/cleanup-aws.yml @@ -1,4 +1,4 @@ -name: cleanup +name: Cleanup AWS S3 Bucket on: pull_request: diff --git a/.github/workflows/cleanup-firebase.yml b/.github/workflows/cleanup-firebase.yml index 82211fab..beaab4b2 100644 --- a/.github/workflows/cleanup-firebase.yml +++ b/.github/workflows/cleanup-firebase.yml @@ -13,17 +13,10 @@ jobs: os: [ubuntu-latest, windows-latest, macOS-latest] steps: - uses: actions/checkout@v4.2.2 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install .[all] + - uses: ./.github/actions/dependencies - name: Cleanup Firebase Metadata env: FIREBASE_TOKEN: ${{ secrets.FIREBASE_TOKEN }} FIREBASE_EMAIL: ${{ secrets.FIREBASE_EMAIL }} run: | - python cellpack/bin/cleanup_tasks.py + pdm run python cellpack/bin/cleanup_tasks.py diff --git a/.github/workflows/make-requirements.yml b/.github/workflows/make-requirements.yml new file mode 100644 index 00000000..09c2c516 --- /dev/null +++ b/.github/workflows/make-requirements.yml @@ -0,0 +1,105 @@ +name: Make requirements files + +on: + workflow_dispatch: + push: + branches: + - main + paths: + - "pdm.lock" + +jobs: + make-requirements: + runs-on: ${{ matrix.os }} + strategy: + matrix: + os: [ubuntu-latest, macOS-latest, windows-latest] + + steps: + - uses: actions/checkout@v4 + - uses: ./.github/actions/pdm + + - name: Generate requirements.txt + shell: bash + run: | + case "${{ matrix.os }}" in + "ubuntu-latest") + export PLATFORM="linux" + ;; + "macOS-latest") + export PLATFORM="macos" + ;; + "windows-latest") + export PLATFORM="windows" + ;; + esac + + rm -rf requirements/* + mkdir -p requirements/$PLATFORM + pdm requirements requirements/$PLATFORM/requirements.txt + + - name: Get platform variable + id: platform + shell: bash + run: | + case "${{ matrix.os }}" in + "ubuntu-latest") + echo "::set-output name=platform::linux" + ;; + "macOS-latest") + echo "::set-output name=platform::macos" + ;; + "windows-latest") + echo "::set-output name=platform::windows" + ;; + esac + + - name: Upload requirements files + uses: actions/upload-artifact@v4 + with: + name: ${{ steps.platform.outputs.platform }}-requirements + path: requirements/${{ steps.platform.outputs.platform }} + + open-PR: + needs: [make-requirements] + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - name: Download linux requirements files + uses: actions/download-artifact@v4 + with: + name: linux-requirements + path: requirements/linux + + - name: Download windows requirements files + uses: actions/download-artifact@v4 + with: + name: windows-requirements + path: requirements/windows + + - name: Download macOS requirements files + uses: actions/download-artifact@v4 + with: + name: macos-requirements + path: requirements/macos + + - name: Clean-up CRLF + shell: bash + run: find requirements -type f -exec sed -i 's/\r//g' {} \; + + - name: Get timestamp + id: timestamp + run: echo "::set-output name=timestamp::$(date +'%Y-%m-%d_%H-%M')" + + - name: Create Pull Request + uses: peter-evans/create-pull-request@v5 + with: + base: main + title: admin/requirements-update_${{ steps.timestamp.outputs.timestamp }} + body: Updating requirements.txt. + + Due to some [challenges](https://github.com/peter-evans/create-pull-request/blob/main/docs/concepts-guidelines.md#triggering-further-workflow-runs), + with getting this PR to trigger the tests, please manually close and re-open this PR. + branch: admin/requirements-update_${{ steps.timestamp.outputs.timestamp }} + commit-message: Updating requirements.txt after change to `pdm.lock` was pushed to `main` + delete-branch: true \ No newline at end of file diff --git a/.gitignore b/.gitignore index 2588d41a..7ae7e8c1 100644 --- a/.gitignore +++ b/.gitignore @@ -74,9 +74,6 @@ target/ .ipynb_checkpoints *.ipynb -# pyenv -.python-version - # celery beat schedule file celerybeat-schedule @@ -122,4 +119,7 @@ data/ **/converted/* # credentials -.creds \ No newline at end of file +.creds + +# pdm files +.pdm-python \ No newline at end of file diff --git a/.python-version b/.python-version new file mode 100644 index 00000000..bd28b9c5 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.9 diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 6196a3de..9b304796 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -15,10 +15,11 @@ Ready to contribute? Here's how to set up `cellpack` for local development. git clone git@github.com:{your_name_here}/cellpack.git ``` -3. Install the project in editable mode. (It is also recommended to work in a virtualenv or anaconda environment): +3. Install the project in editable mode by following installation instructions [here](docs/INSTALL.md). (It is also recommended to work in a virtual environment): ```bash cd cellpack/ + pip install -r requirements/linux/requirements.txt pip install -e .[dev] ``` diff --git a/Makefile b/Makefile index 5ec37f98..c74ec7df 100644 --- a/Makefile +++ b/Makefile @@ -33,6 +33,11 @@ clean: ## clean all build, python, and testing files rm -fr build/ rm -fr dist/ rm -fr .eggs/ + rm -fr .tox/ + rm -fr .coverage + rm -fr coverage.xml + rm -fr htmlcov/ + rm -fr .pytest_cache find . -name '*.egg-info' -exec rm -fr {} + find . -name '*.egg' -exec rm -f {} + find . -name '*.pyc' -exec rm -f {} + @@ -40,11 +45,6 @@ clean: ## clean all build, python, and testing files find . -name '*~' -exec rm -f {} + find . -name '__pycache__' -exec rm -fr {} + find . -name '*.py.bak' -exec rm -f {} + - rm -fr .tox/ - rm -fr .coverage - rm -fr coverage.xml - rm -fr htmlcov/ - rm -fr .pytest_cache build: ## run tox / run tests and lint tox diff --git a/README.md b/README.md index 3fcd8eba..81cefbec 100644 --- a/README.md +++ b/README.md @@ -1,28 +1,41 @@ -# cellPack +# cellPACK [![Continuous Integration](https://github.com/mesoscope/cellpack/actions/workflows/ci.yml/badge.svg)](https://github.com/mesoscope/cellpack/actions/workflows/ci.yml) [![Documentation](https://github.com/mesoscope/cellpack/workflows/Documentation/badge.svg)](https://mesoscope.github.io/cellpack/) [![Code Coverage](https://codecov.io/gh/mesoscope/cellpack/branch/main/graph/badge.svg)](https://codecov.io/gh/mesoscope/cellpack) -algorithm to pack molecular recipes +An algorithm to pack molecular recipes -### Prerequisite -1. Install Conda: https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html - -### Setup -1. create a virtual env: `conda create -n autopack python=3.9` -2. `conda activate autopack` -3. `pip install -e .[dev]` +## Installation -### Run pack code +> [!NOTE] +> These are the basic installation steps. However, our recommendation is to install with `pyenv` and `pdm`. See advanced installation instructions [here](docs/INSTALL.md). + +1. Install Python 3.9 and `git`. Update pip at least to `24.0.0`. +2. Clone this git repository. +```bash +git clone git@github.com:AllenCell/nuc-morph-analysis.git +cd nuc-morph-analysis +``` +3. Create a new virtual environment and activate it. +```bash +python -m venv .venv +source .venv/bin/activate +``` +4. Install the required packages for your operating system. Replace `linux` with `macos` or `windows` as appropriate. +```bash +pip install -r requirements/linux/requirements.txt +pip install -e . +``` + +## Run pack code 1. example pack v1 recipe : `pack -r examples/recipes/v1/NM_Analysis_FigureB1.0.json -c examples/packing-configs/run.json` 2. example pack v2 recipe : `pack -r examples/recipes/v2/one_sphere.json -c examples/packing-configs/run.json` 3. example pack from remote : `pack -r github:recipes/NM_Analysis_FigureB1.0.json -c examples/packing-configs/run.json` -### Run conversion code +## Run conversion code * To convert to simularium and view at https://staging.simularium.allencell.org/viewer `convert -r [FULL_PATH_TO_INPUT_RECIPE_FILE] -p [FULL_PATH_TO_PACKING_RESULT] -o [OUTPUT_PATH]` -## Installation **Stable Release:** `pip install cellpack`
**Development Head:** `pip install git+https://github.com/mesoscope/cellpack.git` @@ -44,8 +57,7 @@ See [CONTRIBUTING.md](CONTRIBUTING.md) for information related to developing the 2. `make build` - This will run `tox` which will run all your tests in both Python 3.7 - and Python 3.8 as well as linting your code. + This will run `tox` which will run all your tests and lint your code. 3. `make clean` @@ -57,7 +69,7 @@ See [CONTRIBUTING.md](CONTRIBUTING.md) for information related to developing the This will generate and launch a web browser to view the most up-to-date documentation for your Python package. -#### Suggested Git Branch Strategy +### Suggested Git Branch Strategy 1. `main` is for the most up-to-date development, very rarely should you directly commit to this branch. GitHub Actions will run on every push and on a CRON to this diff --git a/cellpack/autopack/Graphics.py b/cellpack/autopack/Graphics.py index 6e0dbba6..2a20e19f 100644 --- a/cellpack/autopack/Graphics.py +++ b/cellpack/autopack/Graphics.py @@ -2104,7 +2104,7 @@ def color( data=None, objects=None, colors=[upyColors.red, upyColors.black], - **options + **options, ): mini = None maxi = None @@ -2133,7 +2133,7 @@ def color( objects=objects, ramp=ramp, colors=colors, - **options + **options, ) elif mode == "order": # the order is in the name @@ -2143,7 +2143,7 @@ def color( objects=objects, ramp=ramp, colors=colors, - **options + **options, ) print("datas", len(datas)) print("objs", len(listeObjs)) @@ -2166,7 +2166,7 @@ def colorByDistanceFrom( objects=None, ramp=None, colors=[upyColors.red, upyColors.black], - **options + **options, ): """ target : name or host object target @@ -2240,7 +2240,7 @@ def colorByOrder( objects=None, ramp=None, colors=[upyColors.red, upyColors.black], - **options + **options, ): """ target : name or host object target diff --git a/cellpack/autopack/ingredient/grow.py b/cellpack/autopack/ingredient/grow.py index a0b7a4c9..c8313b4e 100644 --- a/cellpack/autopack/ingredient/grow.py +++ b/cellpack/autopack/ingredient/grow.py @@ -1659,7 +1659,7 @@ def __init__( meshObject=None, orientation=(1, 0, 0), count=0, - **kw + **kw, ): GrowIngredient.__init__( self, @@ -1687,7 +1687,7 @@ def __init__( orientation, count, type, - **kw + **kw, ) if name is None: name = "Actine_%s_%f" % (str(radii), molarity) diff --git a/cellpack/autopack/upy/hostHelper.py b/cellpack/autopack/upy/hostHelper.py index ab89efa4..16786f36 100644 --- a/cellpack/autopack/upy/hostHelper.py +++ b/cellpack/autopack/upy/hostHelper.py @@ -793,7 +793,7 @@ def addLampToScene( shadow=False, center=[0.0, 0.0, 0.0], scene=None, - **kw + **kw, ): """ Add a light to the scene @@ -1651,7 +1651,7 @@ def Text( pos=None, font=None, lookAt=False, - **kw + **kw, ): """ Create a hostobject of type Text. @@ -1809,7 +1809,7 @@ def box( size=[1.0, 1.0, 1.0], cornerPoints=None, visible=1, - **kw + **kw, ): """ Create a hostobject of type cube. @@ -1852,7 +1852,7 @@ def updateBox( cornerPoints=None, visible=1, mat=None, - **kw + **kw, ): """ Update the given box. @@ -1958,7 +1958,7 @@ def plane( size=[1.0, 1.0], cornerPoints=None, visible=1, - **kw + **kw, ): """ Create a hostobject of type cube. @@ -2577,7 +2577,7 @@ def createsNmesh( color=[ [1, 0, 0], ], - **kw + **kw, ): """ Function that generate a Polygon object from the given vertices, face and normal. @@ -2644,7 +2644,7 @@ def addBone( boneParent=None, name=None, editMode=True, - **kw + **kw, ): """ Add one bone to an armature. @@ -2746,7 +2746,7 @@ def particle( radius=None, color=None, hostmatrice=None, - **kw + **kw, ): """ Create a particle system along the given coordinates @@ -4293,7 +4293,7 @@ def setRigidBody( dynamicsAngularDamp=0.0, massClamp=0.0, rotMassClamp=1.0, - **kw + **kw, ): """ Set the curren objec as a rigid body @@ -4326,7 +4326,7 @@ def updateSpring( rlength=0.0, stifness=1.0, damping=1.0, - **kw + **kw, ): """ Update the spring control @@ -4348,7 +4348,7 @@ def createSpring( stifness=1.0, damping=1.0, parent=None, - **kw + **kw, ): """ Create a sprin between two physics objects @@ -4386,7 +4386,7 @@ def get_noise( offset=1.0, octaves=6, gain=1.0, - **kw + **kw, ): # multi_fractal(position, H, lacunarity, octaves, noise_basis=noise.types.STDPERLIN) # NotePlease use InitFbm() before you use one of the following noise types: diff --git a/docs/INSTALL.md b/docs/INSTALL.md new file mode 100644 index 00000000..c9f5021e --- /dev/null +++ b/docs/INSTALL.md @@ -0,0 +1,63 @@ +# Installation with `pyenv` and `pdm` +`pyenv` allows you to install multiple python versions side by side in your local user environment. This installation method is preferred over using `conda` to install `pdm` + +## Install pyenv +1. Install pyenv: Follow the `pyenv` installation instructions [here](https://github.com/pyenv/pyenv#installation). There are just two steps. +1. Download and install `pyenv` +2. Add `pyenv` functions to your shell configuration. + +## Install python 3.9 +Navigate to the `cellPACK` folder and install the required python version. +```bash +pyenv install $(cat .python-version) +``` +The `.python-version` file in this repo tells `pyenv` to load Python 3.9 when you are inside the `cellPACK` directory. +Check that this is working with `which python && python --version`. + +## Install `pdm` +Detailed installation instructions are available [here](https://pdm.fming.dev/latest/#installation). +For Linux or MacOS, install `pdm` for your user as follows. + +1. Download the installer + +```bash +curl -sSLO https://pdm.fming.dev/install-pdm.py +``` + +2. Validate that the installer has not been tampered with + +```bash +curl -sSL https://pdm.fming.dev/install-pdm.py.sha256 | shasum -a 256 -c - +``` + +3. Using Python 3.9, run the installer. + +```bash +python install-pdm.py +``` +> [!WARNING] +> With this installation method `pdm` will be tied to the exact python version used to install it. If you installed with Python 3.9.13, for example, and you later transition to Python 3.9.17, do not uninstall Python 3.9.13. + +`pdm` will be installed into `$HOME/.local/bin`. Check that your version is at least 2.10. +```bash +$ pdm --version +PDM, version 2.10.4 +``` + +## Install the project dependencies +From the `cellPACK` directory, use `pdm` to install the dependencies. +```bash +pdm sync -d +``` + +This will create a virtual environment at `cellPACK/.venv`. You can activate it with `eval $(pdm venv activate)` or `source .venv/bin/activate`. + +## Managing dependencies with `pdm` +To modify the project dependencies, see [our instructions for using pdm](pdm.md). + + +# Testing +To run the tests: +```bash +pdm run pytest +``` \ No newline at end of file diff --git a/docs/pdm.md b/docs/pdm.md new file mode 100644 index 00000000..b9b43b72 --- /dev/null +++ b/docs/pdm.md @@ -0,0 +1,30 @@ +# Using PDM +These instructions are intended to get you started managing dependencies with PDM. Consult the [PDM documentation](https://pdm.fming.dev/latest/usage/dependency/) for more detailed help. + +## Workflow for adding/updating/removing a package +1. To add/update/remove a package, use a Linux machine. The `pdm.lock` file is _usually_ compatible across operating systems, but in some cases `pdm` can generate a lock file that is only compatible with the operating system family used to generate it. Ours should always be compatible with Linux. + +2. Start a new branch from `main` (`git checkout main && git checkout -b {branch-name}`), or if you are already on a branch, get the latest changes from the `main` to avoid merge conflicts with `pdm.lock` (`git merge main`). + +3. Synchronize the current installed dependencies with the lock file. +```bash +pdm sync +``` + +4. Update `pyproject.toml` and `pdm.lock`. This will install/update/uninstall the package from your current virtual environment. +```bash +# Add package(s) to pyproject.toml and install them +pdm add {package-name} +# Remove packages from pyproject.toml +pdm remove {package-name} +# Update all packages according to pyproject.toml +pdm update +# Update one package +pdm update {package-name} +``` + +5. Test and commit your changes to `pyproject.toml` and `pdm.lock`. + +6. Make a pull request on Github with your changes and (after approval) merge it. + +7. A Github action will make a second pull request to update all three `requirements/{platform}/requirements.txt` files based on your changes. 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+keywords = ["cellpack"] +readme = "README.md" +authors = [ + {name = "Megan Riel-Mehan", email = "meganr@alleninstitute.org"}, + {name = "Saurabh Mogre", email = "saurabh.mogre@alleninstitute.org"}, + {name = "Ruge Li", email = "ruge.li@alleninstitute.org"}, +] +classifiers = [ + "Development Status :: 2 - Pre-Alpha", + "Intended Audience :: Developers", + "License :: OSI Approved :: MIT License", + "Natural Language :: English", + "Programming Language :: Python :: 3.9", +] +requires-python = "==3.9.*" +dependencies = [ + "aicsimageio>=4.10.0", + "boto3>=1.28.3", + "deepdiff>=5.5.0", + "fire>=0.4.0", + "firebase_admin>=6.0.1", + "matplotlib>=3.3.4", + "mdutils>=1.4.0", + "moto>=5.0.2", + "numpy>=1.19.2", + "plotly>=5.3.1", + "pycollada>=0.7.1", + "pymunk>=6.2.0", + "python-dotenv>=1.0.0", + "rtree", + "scikit-learn>=1.1.3", + "scipy>=1.6.2", + "seaborn>=0.12.1", + "simulariumio>=1.6.3", + "tqdm>=4.64.1", + "trimesh>=3.9.34", +] +license = {text = "MIT license"} + +[project.urls] +Homepage = "https://github.com/mesoscope/cellpack" + +[project.scripts] +analyze = "cellpack.bin.analyze:main" +convert = "cellpack.bin.simularium_converter:main" +pack = "cellpack.bin.pack:main" +upload = "cellpack.bin.upload:main" +clean = "cellpack.bin.clean:main" + +[tool.pdm.dev-dependencies] +setup = [ + "pytest-runner>=5.2", +] +test = [ + "pytest-cov>=2.9.0", + "pytest-raises>=0.11", + "pytest>=5.4.3", +] +lint = [ + "black>=19.10b0, <=24.8.0", + "flake8-debugger>=3.2.1", + "flake8>=3.8.3, <=6.0.0", +] +dev = [ + "Sphinx>=3.4.3", + "bump2version>=1.0.1", + "coverage>=5.1", + "ipython>=7.15.0", + "m2r2>=0.2.7", + "sphinx_rtd_theme>=0.5.1", + "tox>=3.15.2", + "wheel>=0.34.2", + "tox-pdm>=0.7.2", +] + +[tool.pdm.scripts] +requirements = "pdm export -f requirements --without-hashes -o" + +[tool.black] +line-length = 88 + +[build-system] +requires = ["pdm-backend"] +build-backend = "pdm.backend" \ No newline at end of file diff --git a/requirements/linux/requirements.txt b/requirements/linux/requirements.txt new file mode 100644 index 00000000..b5646963 --- /dev/null +++ b/requirements/linux/requirements.txt @@ -0,0 +1,193 @@ +# This file is @generated by PDM. +# Please do not edit it manually. + +aicsimageio==4.14.0 +aiohappyeyeballs==2.4.3 +aiohttp==3.10.10 +aiosignal==1.3.1 +alabaster==0.7.16 +annotated-types==0.7.0 +appdirs==1.4.4 +asciitree==0.3.3 +asttokens==2.4.1 +async-timeout==4.0.3; python_version < "3.11" +attrs==24.2.0 +babel==2.16.0 +black==22.12.0 +boto3==1.35.42 +botocore==1.35.42 +bump2version==1.0.1 +cachecontrol==0.14.0 +cachetools==5.5.0 +certifi==2024.8.30 +cffi==1.17.1 +chardet==5.2.0 +charset-normalizer==3.4.0 +click==8.1.7 +cloudpickle==3.1.0 +colorama==0.4.6 +contourpy==1.3.0 +coverage[toml]==7.6.3 +cryptography==43.0.1 +cycler==0.12.1 +dask[array]==2024.8.0 +decorator==5.1.1 +deepdiff==8.0.1 +distlib==0.3.9 +distributed==2024.8.0 +docutils==0.21.2 +elementpath==4.5.0 +exceptiongroup==1.2.2; python_version < "3.11" 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platform_python_implementation != "PyPy" +grpcio-status==1.67.0; platform_python_implementation != "PyPy" +httplib2==0.22.0 +idna==3.10 +imagecodecs==2024.9.22 +imageio==2.36.0 +imagesize==1.4.1 +importlib-metadata==8.5.0; python_version < "3.12" +importlib-resources==6.4.5; python_version < "3.10" +iniconfig==2.0.0 +ipython==8.18.1 +jedi==0.19.1 +jinja2==3.1.4 +jmespath==1.0.1 +joblib==1.4.2 +kiwisolver==1.4.7 +lazy-loader==0.4 +locket==1.0.0 +lxml==4.9.4 +m2r2==0.3.3.post2 +markupsafe==3.0.1 +matplotlib==3.9.2 +matplotlib-inline==0.1.7 +mccabe==0.7.0 +mdutils==1.6.0 +mistune==0.8.4 +moto==5.0.17 +msgpack==1.1.0 +multidict==6.1.0 +mypy-extensions==1.0.0 +networkx==3.2.1 +numcodecs==0.12.1 +numpy==2.0.2 +ome-types==0.5.2 +ome-zarr==0.9.0 +orderly-set==5.2.2 +packaging==24.1 +pandas==2.2.3 +parso==0.8.4 +partd==1.4.2 +pathspec==0.12.1 +pexpect==4.9.0; sys_platform != "win32" +pillow==11.0.0 +pint==0.24.3 +platformdirs==4.3.6 +plotly==5.24.1 +pluggy==1.5.0 +prompt-toolkit==3.0.48 +propcache==0.2.0 +proto-plus==1.24.0 +protobuf==5.28.2 +psutil==6.0.0 +ptyprocess==0.7.0; sys_platform != "win32" +pure-eval==0.2.3 +pyasn1==0.6.1 +pyasn1-modules==0.4.1 +pycodestyle==2.10.0 +pycollada==0.8 +pycparser==2.22 +pydantic==2.9.2 +pydantic-compat==0.1.2 +pydantic-core==2.23.4 +pyflakes==3.0.1 +pygments==2.18.0 +pyjwt[crypto]==2.9.0 +pymunk==6.9.0 +pyparsing==3.2.0 +pyproject-api==1.8.0 +pytest==8.3.3 +pytest-cov==5.0.0 +pytest-raises==0.11 +pytest-runner==6.0.1 +python-dateutil==2.9.0.post0 +python-dotenv==1.0.1 +pytz==2024.2 +pyyaml==6.0.2 +requests==2.32.3 +resource-backed-dask-array==0.1.0 +responses==0.25.3 +rsa==4.9 +rtree==1.3.0 +s3fs==0.4.2 +s3transfer==0.10.3 +scikit-image==0.24.0 +scikit-learn==1.5.2 +scipy==1.13.1 +seaborn==0.13.2 +simulariumio==1.11.0 +six==1.16.0 +snowballstemmer==2.2.0 +sortedcontainers==2.4.0 +sphinx==7.4.7 +sphinx-rtd-theme==3.0.1 +sphinxcontrib-applehelp==2.0.0 +sphinxcontrib-devhelp==2.0.0 +sphinxcontrib-htmlhelp==2.1.0 +sphinxcontrib-jquery==4.1 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==2.0.0 +sphinxcontrib-serializinghtml==2.0.0 +stack-data==0.6.3 +tblib==3.0.0 +tenacity==9.0.0 +termcolor==2.5.0 +threadpoolctl==3.5.0 +tifffile==2023.2.28 +tomli==2.0.2; python_version < "3.11" +toolz==1.0.0 +tornado==6.4.1 +tox==4.23.0 +tox-pdm==0.7.2 +tqdm==4.66.5 +traitlets==5.14.3 +trimesh==4.5.0 +typing-extensions==4.12.2 +tzdata==2024.2 +uritemplate==4.1.1 +urllib3==1.26.20 +virtualenv==20.26.6 +wcwidth==0.2.13 +werkzeug==3.0.4 +wheel==0.44.0 +wrapt==1.16.0 +xarray==2024.7.0 +xmlschema==3.4.2 +xmltodict==0.14.2 +xsdata==24.3.1 +yarl==1.15.4 +zarr==2.15.0 +zict==3.0.0 +zipp==3.20.2; python_version < "3.12" diff --git a/requirements/windows/requirements.txt b/requirements/windows/requirements.txt new file mode 100644 index 00000000..b5646963 --- /dev/null +++ b/requirements/windows/requirements.txt @@ -0,0 +1,193 @@ +# This file is @generated by PDM. +# Please do not edit it manually. + +aicsimageio==4.14.0 +aiohappyeyeballs==2.4.3 +aiohttp==3.10.10 +aiosignal==1.3.1 +alabaster==0.7.16 +annotated-types==0.7.0 +appdirs==1.4.4 +asciitree==0.3.3 +asttokens==2.4.1 +async-timeout==4.0.3; python_version < "3.11" +attrs==24.2.0 +babel==2.16.0 +black==22.12.0 +boto3==1.35.42 +botocore==1.35.42 +bump2version==1.0.1 +cachecontrol==0.14.0 +cachetools==5.5.0 +certifi==2024.8.30 +cffi==1.17.1 +chardet==5.2.0 +charset-normalizer==3.4.0 +click==8.1.7 +cloudpickle==3.1.0 +colorama==0.4.6 +contourpy==1.3.0 +coverage[toml]==7.6.3 +cryptography==43.0.1 +cycler==0.12.1 +dask[array]==2024.8.0 +decorator==5.1.1 +deepdiff==8.0.1 +distlib==0.3.9 +distributed==2024.8.0 +docutils==0.21.2 +elementpath==4.5.0 +exceptiongroup==1.2.2; python_version < "3.11" +executing==2.1.0 +fasteners==0.19 +filelock==3.16.1 +fire==0.7.0 +firebase-admin==6.5.0 +flake8==6.0.0 +flake8-debugger==4.1.2 +flexcache==0.3 +flexparser==0.3.1 +fonttools==4.54.1 +frozenlist==1.4.1 +fsspec[s3]==2023.6.0 +google-api-core[grpc]==2.21.0; platform_python_implementation != "PyPy" +google-api-python-client==2.149.0 +google-auth==2.35.0 +google-auth-httplib2==0.2.0 +google-cloud-core==2.4.1 +google-cloud-firestore==2.19.0; platform_python_implementation != "PyPy" +google-cloud-storage==2.18.2 +google-crc32c==1.6.0 +google-resumable-media==2.7.2 +googleapis-common-protos==1.65.0 +grpcio==1.67.0; platform_python_implementation != "PyPy" +grpcio-status==1.67.0; platform_python_implementation != "PyPy" +httplib2==0.22.0 +idna==3.10 +imagecodecs==2024.9.22 +imageio==2.36.0 +imagesize==1.4.1 +importlib-metadata==8.5.0; python_version < "3.12" +importlib-resources==6.4.5; python_version < "3.10" +iniconfig==2.0.0 +ipython==8.18.1 +jedi==0.19.1 +jinja2==3.1.4 +jmespath==1.0.1 +joblib==1.4.2 +kiwisolver==1.4.7 +lazy-loader==0.4 +locket==1.0.0 +lxml==4.9.4 +m2r2==0.3.3.post2 +markupsafe==3.0.1 +matplotlib==3.9.2 +matplotlib-inline==0.1.7 +mccabe==0.7.0 +mdutils==1.6.0 +mistune==0.8.4 +moto==5.0.17 +msgpack==1.1.0 +multidict==6.1.0 +mypy-extensions==1.0.0 +networkx==3.2.1 +numcodecs==0.12.1 +numpy==2.0.2 +ome-types==0.5.2 +ome-zarr==0.9.0 +orderly-set==5.2.2 +packaging==24.1 +pandas==2.2.3 +parso==0.8.4 +partd==1.4.2 +pathspec==0.12.1 +pexpect==4.9.0; sys_platform != "win32" +pillow==11.0.0 +pint==0.24.3 +platformdirs==4.3.6 +plotly==5.24.1 +pluggy==1.5.0 +prompt-toolkit==3.0.48 +propcache==0.2.0 +proto-plus==1.24.0 +protobuf==5.28.2 +psutil==6.0.0 +ptyprocess==0.7.0; sys_platform != "win32" +pure-eval==0.2.3 +pyasn1==0.6.1 +pyasn1-modules==0.4.1 +pycodestyle==2.10.0 +pycollada==0.8 +pycparser==2.22 +pydantic==2.9.2 +pydantic-compat==0.1.2 +pydantic-core==2.23.4 +pyflakes==3.0.1 +pygments==2.18.0 +pyjwt[crypto]==2.9.0 +pymunk==6.9.0 +pyparsing==3.2.0 +pyproject-api==1.8.0 +pytest==8.3.3 +pytest-cov==5.0.0 +pytest-raises==0.11 +pytest-runner==6.0.1 +python-dateutil==2.9.0.post0 +python-dotenv==1.0.1 +pytz==2024.2 +pyyaml==6.0.2 +requests==2.32.3 +resource-backed-dask-array==0.1.0 +responses==0.25.3 +rsa==4.9 +rtree==1.3.0 +s3fs==0.4.2 +s3transfer==0.10.3 +scikit-image==0.24.0 +scikit-learn==1.5.2 +scipy==1.13.1 +seaborn==0.13.2 +simulariumio==1.11.0 +six==1.16.0 +snowballstemmer==2.2.0 +sortedcontainers==2.4.0 +sphinx==7.4.7 +sphinx-rtd-theme==3.0.1 +sphinxcontrib-applehelp==2.0.0 +sphinxcontrib-devhelp==2.0.0 +sphinxcontrib-htmlhelp==2.1.0 +sphinxcontrib-jquery==4.1 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==2.0.0 +sphinxcontrib-serializinghtml==2.0.0 +stack-data==0.6.3 +tblib==3.0.0 +tenacity==9.0.0 +termcolor==2.5.0 +threadpoolctl==3.5.0 +tifffile==2023.2.28 +tomli==2.0.2; python_version < "3.11" +toolz==1.0.0 +tornado==6.4.1 +tox==4.23.0 +tox-pdm==0.7.2 +tqdm==4.66.5 +traitlets==5.14.3 +trimesh==4.5.0 +typing-extensions==4.12.2 +tzdata==2024.2 +uritemplate==4.1.1 +urllib3==1.26.20 +virtualenv==20.26.6 +wcwidth==0.2.13 +werkzeug==3.0.4 +wheel==0.44.0 +wrapt==1.16.0 +xarray==2024.7.0 +xmlschema==3.4.2 +xmltodict==0.14.2 +xsdata==24.3.1 +yarl==1.15.4 +zarr==2.15.0 +zict==3.0.0 +zipp==3.20.2; python_version < "3.12" diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index d9421992..00000000 --- a/setup.cfg +++ /dev/null @@ -1,32 +0,0 @@ -[bumpversion] -current_version = 1.0.8 -commit = True -tag = True - -[bumpversion:file:setup.py] -search = version="{current_version}" -replace = version="{new_version}" - -[bumpversion:file:cellpack/__init__.py] -search = {current_version} -replace = {new_version} - -[bdist_wheel] -universal = 1 - -[aliases] -test = pytest - -[tool:pytest] -addopts = --ignore=setup.py - -[flake8] -exclude = - docs/ -ignore = - E203 - E402 - W291 - W503 - E501 -max-line-length = 88 diff --git a/setup.py b/setup.py deleted file mode 100644 index 885b4117..00000000 --- a/setup.py +++ /dev/null @@ -1,124 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- - -"""The setup script.""" - -from setuptools import find_packages, setup - -with open("README.md") as readme_file: - readme = readme_file.read() - -setup_requirements = [ - "pytest-runner>=5.2", -] - -test_requirements = [ - "black>=19.10b0, <=24.8.0", - "flake8>=3.8.3, <=6.0.0", - "flake8-debugger>=3.2.1", - "pytest>=5.4.3", - "pytest-cov>=2.9.0", - "pytest-raises>=0.11", -] - -analysis_requirements = [ - "tqdm>=4.64.1", - "mdutils>=1.4.0", - "scikit-learn>=1.1.3", - "seaborn>=0.12.1", - "aicsimageio>=4.10.0", - "pandas>=1.2.4", -] - -dev_requirements = [ - *setup_requirements, - *test_requirements, - *analysis_requirements, - "bump2version>=1.0.1", - "coverage>=5.1", - "ipython>=7.15.0", - "m2r2>=0.2.7", - "pytest-runner>=5.2", - "Sphinx>=3.4.3", - "sphinx_rtd_theme>=0.5.1", - "tox>=3.15.2", - "twine>=3.1.1", - "wheel>=0.34.2", -] - -requirements = [ - *analysis_requirements, - "boto3>=1.28.3", - "fire>=0.4.0", - "firebase_admin>=6.0.1", - "matplotlib>=3.3.4", - "numpy>=1.19.2", - "scipy>=1.6.2", - "simulariumio>=1.6.3", - "plotly>=5.3.1", - "pycollada>=0.7.1", - "pymunk>=6.2.0", - "rtree", - "trimesh>=3.9.34", - "deepdiff>=5.5.0", - "python-dotenv>=1.0.0", - "moto>=5.0.2", -] - -extra_requirements = { - "setup": setup_requirements, - "test": test_requirements, - "dev": dev_requirements, - "all": [ - *requirements, - *dev_requirements, - ], -} - -setup( - author="Megan Riel-Mehan", - author_email="meganr@alleninstitute.org", - classifiers=[ - "Development Status :: 2 - Pre-Alpha", - "Intended Audience :: Developers", - "License :: OSI Approved :: MIT License", - "Natural Language :: English", - "Programming Language :: Python :: 3.7", - "Programming Language :: Python :: 3.8", - "Programming Language :: Python :: 3.9", - ], - description="algorithm to pack molecular recipes", - entry_points={ - "console_scripts": [ - "analyze=cellpack.bin.analyze:main", - "convert=cellpack.bin.simularium_converter:main", - "upload=cellpack.bin.upload:main", - "pack=cellpack.bin.pack:main", - ] - }, - install_requires=requirements, - license="MIT license", - long_description=readme, - long_description_content_type="text/markdown", - include_package_data=True, - keywords="cellpack", - name="cellpack", - packages=find_packages(exclude=["tests", "*.tests", "*.tests.*"]), - package_data={ - "": [ - "cellpack/tests/packing-configs/*", - "cellpack/tests/recipes/*", - "logging.conf", - ] - }, - python_requires=">=3.8", - setup_requires=setup_requirements, - test_suite="cellpack/tests", - tests_require=test_requirements, - extras_require=extra_requirements, - url="https://github.com/mesoscope/cellpack", - # Do not edit this string manually, always use bumpversion - # Details in CONTRIBUTING.rst - version="1.0.8", - zip_safe=False, -) diff --git a/tox.ini b/tox.ini index 9b83fd7e..0efa77d2 100644 --- a/tox.ini +++ b/tox.ini @@ -1,19 +1,14 @@ [tox] -skipsdist = True -envlist = py38, py39, lint -[flake8] -ignore = E501,E277,W503,E203 +env_list = py39, lint +base_python = python3.9 + [testenv:lint] -deps = - .[test] +groups = lint commands = flake8 cellpack --count --verbose --show-source --statistics --ignore=E501,E277,W503,E203 black --check cellpack [testenv] -setenv = - PYTHONPATH = {toxinidir} -deps = - .[test] +groups = dev commands = pytest --basetemp={envtmpdir} --cov-report html --cov=cellpack cellpack/tests/