From 838235a20d129cafe9026f7909988ff222edd181 Mon Sep 17 00:00:00 2001 From: Saurabh Mogre Date: Tue, 15 Oct 2024 15:21:52 -0700 Subject: [PATCH 01/21] Update README.md --- README.md | 67 ++++++++++++++++++++++++++++++++++++++++++++++--------- 1 file changed, 56 insertions(+), 11 deletions(-) diff --git a/README.md b/README.md index 3fcd8eba..deebe220 100644 --- a/README.md +++ b/README.md @@ -1,28 +1,73 @@ -# 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 +## Installation + +### 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 $(cat .python-version) +``` +The `.python-version` file in this repo tells `pyenv` to load Python 3.9 when you are inside the `cellPACK` directory. +Check that this is working with `which python && python --version`. + +### Install `pdm` +Detailed installation instructions are available [here](https://pdm.fming.dev/latest/#installation). +For Linux or MacOS, install `pdm` for your user as follows. + +1. Download the installer + +```bash +curl -sSLO https://pdm.fming.dev/install-pdm.py +``` + +2. Validate that the installer has not been tampered with -### Setup -1. create a virtual env: `conda create -n autopack python=3.9` -2. `conda activate autopack` -3. `pip install -e .[dev]` +```bash +curl -sSL https://pdm.fming.dev/install-pdm.py.sha256 | shasum -a 256 -c - +``` -### Run pack code +3. Using Python 3.9, run the installer. + +```bash +python install-pdm.py +``` +> [!WARNING] +> With this installation method `pdm` will be tied to the exact python version used to install it. If you installed with Python 3.9.13, for example, and you later transition to Python 3.9.17, do not uninstall Python 3.9.13. + +`pdm` will be installed into `$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`. + + +## 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` From 915f4913d86f32f141b52512950d4c0010809138 Mon Sep 17 00:00:00 2001 From: Saurabh Mogre Date: Tue, 15 Oct 2024 15:36:21 -0700 Subject: [PATCH 02/21] Remove setup.py and setup.cfg --- setup.cfg | 32 -------------- setup.py | 124 ------------------------------------------------------ 2 files changed, 156 deletions(-) delete mode 100644 setup.cfg delete mode 100644 setup.py 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", - 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"pycollada>=0.7.1", + "pymunk>=6.2.0", + "pytest-cov>=2.9.0", + "pytest-raises>=0.11", + "pytest-runner>=5.2", + "pytest-runner>=5.2", + "pytest>=5.4.3", + "python-dotenv>=1.0.0", + "rtree", + "scikit-learn>=1.1.3", + "scikit-learn>=1.1.3", + "scipy>=1.6.2", + "seaborn>=0.12.1", + "seaborn>=0.12.1", + "simulariumio>=1.6.3", + "sphinx_rtd_theme>=0.5.1", + "tox>=3.15.2", + "tqdm>=4.64.1", + "tqdm>=4.64.1", + "trimesh>=3.9.34", + "twine>=3.1.1", + "wheel>=0.34.2", +] + +[project.scripts] +analyze = "cellpack.bin.analyze:main" +convert = "cellpack.bin.simularium_converter:main" +pack = "cellpack.bin.pack:main" +upload = "cellpack.bin.upload:main" + +[build-system] +requires = ["pdm-backend"] +build-backend = "pdm.backend" From cc7b51a3cab691881718b106fb14e088732fb291 Mon Sep 17 00:00:00 2001 From: Saurabh Mogre Date: Tue, 15 Oct 2024 15:36:57 -0700 Subject: [PATCH 04/21] Update .gitignore --- .gitignore | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) 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 From bb64e0f0f56ad81115a0a2b09fa0f30aea462214 Mon Sep 17 00:00:00 2001 From: Saurabh Mogre Date: Wed, 16 Oct 2024 15:21:21 -0700 Subject: [PATCH 05/21] Add requirements files --- requirements/linux/requirements.txt | 1887 +++++++++++++++++++++++++ requirements/macos/requirements.txt | 1887 +++++++++++++++++++++++++ requirements/windows/requirements.txt | 1887 +++++++++++++++++++++++++ 3 files changed, 5661 insertions(+) create mode 100644 requirements/linux/requirements.txt create mode 100644 requirements/macos/requirements.txt create mode 100644 requirements/windows/requirements.txt diff --git a/requirements/linux/requirements.txt b/requirements/linux/requirements.txt new file mode 100644 index 00000000..9b163779 --- /dev/null +++ b/requirements/linux/requirements.txt @@ -0,0 +1,1887 @@ +# This file is @generated by PDM. +# Please do not edit it manually. + +aicsimageio==4.14.0 \ + --hash=sha256:0f6684587b1d833ce5b10f3e81314e2a89269cd94bd09747fcd6460f3119855c \ + --hash=sha256:b3df2beba7d000c35660816116d562bfe96ed2beb79713b023a7579e5e72c646 +aiohappyeyeballs==2.4.3 \ + --hash=sha256:75cf88a15106a5002a8eb1dab212525c00d1f4c0fa96e551c9fbe6f09a621586 \ + --hash=sha256:8a7a83727b2756f394ab2895ea0765a0a8c475e3c71e98d43d76f22b4b435572 +aiohttp==3.10.10 \ + --hash=sha256:007ec22fbc573e5eb2fb7dec4198ef8f6bf2fe4ce20020798b2eb5d0abda6138 \ + --hash=sha256:00819de9e45d42584bed046314c40ea7e9aea95411b38971082cad449392b08c \ + --hash=sha256:01948b1d570f83ee7bbf5a60ea2375a89dfb09fd419170e7f5af029510033d24 \ + --hash=sha256:05646ebe6b94cc93407b3bf34b9eb26c20722384d068eb7339de802154d61bc5 \ + 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--hash=sha256:a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350 \ + --hash=sha256:bc9eb26f4506fda01b81bcde0ca78103b6e62f991b381fec825435c836edbc29 From 4986096ee28219e8fb22650c83855c71242f1d54 Mon Sep 17 00:00:00 2001 From: Saurabh Mogre Date: Wed, 16 Oct 2024 15:22:29 -0700 Subject: [PATCH 06/21] Update installation instructions to remove conda --- README.md | 63 ++++++++++++------------------------------------- docs/INSTALL.md | 63 +++++++++++++++++++++++++++++++++++++++++++++++++ docs/pdm.md | 30 +++++++++++++++++++++++ 3 files changed, 108 insertions(+), 48 deletions(-) create mode 100644 docs/INSTALL.md create mode 100644 docs/pdm.md diff --git a/README.md b/README.md index deebe220..2f368904 100644 --- a/README.md +++ b/README.md @@ -8,57 +8,25 @@ An algorithm to pack molecular recipes ## Installation -### 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. +> [!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). -### Install python 3.9 -Navigate to the `cellPACK` folder and install the required python version. +1. Install Python 3.9 and `git`. Update pip at least to `24.0.0`. +2. Clone this git repository. ```bash -pyenv install $(cat .python-version) +git clone git@github.com:AllenCell/nuc-morph-analysis.git +cd nuc-morph-analysis ``` -The `.python-version` file in this repo tells `pyenv` to load Python 3.9 when you are inside the `cellPACK` directory. -Check that this is working with `which python && python --version`. - -### Install `pdm` -Detailed installation instructions are available [here](https://pdm.fming.dev/latest/#installation). -For Linux or MacOS, install `pdm` for your user as follows. - -1. Download the installer - +3. Create a new virtual environment and activate it. ```bash -curl -sSLO https://pdm.fming.dev/install-pdm.py +python -m venv .venv +source .venv/bin/activate ``` - -2. Validate that the installer has not been tampered with - -```bash -curl -sSL https://pdm.fming.dev/install-pdm.py.sha256 | shasum -a 256 -c - -``` - -3. Using Python 3.9, run the installer. - +4. Install the required packages for your operating system. Replace `linux` with `macos` or `windows` as appropriate. ```bash -python install-pdm.py +pip install -r requirements/linux/requirements.txt +pip install -e . ``` -> [!WARNING] -> With this installation method `pdm` will be tied to the exact python version used to install it. If you installed with Python 3.9.13, for example, and you later transition to Python 3.9.17, do not uninstall Python 3.9.13. - -`pdm` will be installed into `$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`. - ## Run pack code 1. example pack v1 recipe : `pack -r examples/recipes/v1/NM_Analysis_FigureB1.0.json -c examples/packing-configs/run.json` @@ -82,15 +50,14 @@ See [CONTRIBUTING.md](CONTRIBUTING.md) for information related to developing the ### Contributing cheat sheet -1. `pip install -e .[dev]` +1. `pdm sync -d` This will install your package in editable mode with all the required development dependencies (i.e. `tox`). 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` @@ -102,7 +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/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..5bb4506d --- /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 [like this one](https://github.com/aics-int/nuc-morph-analysis/pull/124) to update all three `requirements/{platform}/requirements.txt` files based on your changes. This second PR must be merged before any further changes are made to `pdm.lock`. \ No newline at end of file From b896046095a20f64ef3ec2beb22db60c87bb6a24 Mon Sep 17 00:00:00 2001 From: Saurabh Mogre Date: Wed, 16 Oct 2024 15:22:55 -0700 Subject: [PATCH 07/21] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 2f368904..81cefbec 100644 --- a/README.md +++ b/README.md @@ -50,7 +50,7 @@ See [CONTRIBUTING.md](CONTRIBUTING.md) for information related to developing the ### Contributing cheat sheet -1. `pdm sync -d` +1. `pip install -e .[dev]` This will install your package in editable mode with all the required development dependencies (i.e. `tox`). From 0f9f5b15f114b5e84580a08c8ffc6825fed9fc3c Mon Sep 17 00:00:00 2001 From: Saurabh Mogre Date: Thu, 17 Oct 2024 12:07:02 -0700 Subject: [PATCH 08/21] Rename cleanup workflow for clarity --- .github/workflows/{cleanup.yml => cleanup-aws.yml} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename .github/workflows/{cleanup.yml => cleanup-aws.yml} (96%) 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 13fc4b52..c920ee31 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: From 5912c042eec0658f47d8f596f22aa078bc05a369 Mon Sep 17 00:00:00 2001 From: Saurabh Mogre Date: Thu, 17 Oct 2024 12:07:34 -0700 Subject: [PATCH 09/21] Update installation instructions in CONTRIBUTING.md --- CONTRIBUTING.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) 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] ``` From f7854cb8b5046bbf2983d9c6d5c370ac20e488a6 Mon Sep 17 00:00:00 2001 From: Saurabh Mogre Date: Thu, 17 Oct 2024 12:07:58 -0700 Subject: [PATCH 10/21] Refactor tox.ini: Update env_list and groups --- tox.ini | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/tox.ini b/tox.ini index 9b83fd7e..64effe1c 100644 --- a/tox.ini +++ b/tox.ini @@ -1,19 +1,13 @@ [tox] -skipsdist = True -envlist = py38, py39, lint -[flake8] -ignore = E501,E277,W503,E203 +env_list = py39, lint + [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/ From 427f396d50dc9baaf289e278ef1a0c3f3b4c85d0 Mon Sep 17 00:00:00 2001 From: Saurabh Mogre Date: Thu, 17 Oct 2024 12:08:36 -0700 Subject: [PATCH 11/21] Add PDM and Dependencies actions Update build-docs workflow Add cache-dependencies workflow Update cleanup-firebase workflow Update ci workflow Update analyze workflow Update analyze workflow --- .github/actions/dependencies/action.yml | 11 +++ .github/actions/pdm/action.yml | 11 +++ .github/workflows/analyze.yml | 16 +--- .github/workflows/build-docs.yml | 13 +-- .github/workflows/cache-dependencies.yml | 18 ++++ .github/workflows/ci.yml | 38 +------- .github/workflows/cleanup-firebase.yml | 9 +- .github/workflows/make-requirements.yml | 105 +++++++++++++++++++++++ 8 files changed, 156 insertions(+), 65 deletions(-) create mode 100644 .github/actions/dependencies/action.yml create mode 100644 .github/actions/pdm/action.yml create mode 100644 .github/workflows/cache-dependencies.yml create mode 100644 .github/workflows/make-requirements.yml diff --git a/.github/actions/dependencies/action.yml b/.github/actions/dependencies/action.yml new file mode 100644 index 00000000..7016a94e --- /dev/null +++ b/.github/actions/dependencies/action.yml @@ -0,0 +1,11 @@ +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 eeee2d57..184e7239 100644 --- a/.github/workflows/analyze.yml +++ b/.github/workflows/analyze.yml @@ -16,17 +16,9 @@ jobs: os: [ubuntu-latest] steps: - uses: actions/checkout@v4 - - 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 + shell: bash 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 @@ -36,7 +28,7 @@ jobs: - 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 - name: Upload results - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: results path: cellpack/tests/outputs/test_spheres/ @@ -59,7 +51,7 @@ 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 diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml index f71fcb2e..f9c0e254 100644 --- a/.github/workflows/build-docs.yml +++ b/.github/workflows/build-docs.yml @@ -10,19 +10,10 @@ jobs: if: ${{ !contains(github.event.head_commit.message, 'Bump version') }} runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2.3.1 + - uses: actions/checkout@v4 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 ce225566..cfbe2046 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -31,16 +31,7 @@ jobs: steps: - uses: actions/checkout@v4 - - 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/ @@ -52,16 +43,7 @@ jobs: if: ${{ !contains(github.event.head_commit.message, 'Bump version') }} steps: - uses: actions/checkout@v4 - - 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 @@ -81,19 +63,7 @@ jobs: steps: - uses: actions/checkout@v4 - - 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-firebase.yml b/.github/workflows/cleanup-firebase.yml index fb8f5849..4bbebb94 100644 --- a/.github/workflows/cleanup-firebase.yml +++ b/.github/workflows/cleanup-firebase.yml @@ -13,14 +13,7 @@ jobs: os: [ubuntu-latest, windows-latest, macOS-latest] steps: - uses: actions/checkout@v4 - - 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 }} 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 From 3c4c2067ef9e3b3a92d78d455811a154f1fb4c6a Mon Sep 17 00:00:00 2001 From: Saurabh Mogre Date: Thu, 17 Oct 2024 12:09:07 -0700 Subject: [PATCH 12/21] Update pyproject.toml dependencies and add pdm lock file --- pdm.lock | 2061 ++++++++++++++++++++---------------------------- pyproject.toml | 90 +-- 2 files changed, 881 insertions(+), 1270 deletions(-) diff --git a/pdm.lock b/pdm.lock index 8ec7d5ad..7293795b 100644 --- a/pdm.lock +++ b/pdm.lock @@ -2,13 +2,13 @@ # It is not intended for manual editing. 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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 :: 3.7", - "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", ] -requires-python = ">=3.9" +requires-python = "==3.9.*" dependencies = [ "aicsimageio>=4.10.0", "boto3>=1.28.3", @@ -29,7 +27,6 @@ dependencies = [ "mdutils>=1.4.0", "moto>=5.0.2", "numpy>=1.19.2", - "pandas>=1.2.4", "plotly>=5.3.1", "pycollada>=0.7.1", "pymunk>=6.2.0", @@ -47,96 +44,41 @@ license = {text = "MIT license"} [project.urls] Homepage = "https://github.com/mesoscope/cellpack" -[project.optional-dependencies] +[project.scripts] +analyze = "cellpack.bin.analyze:main" +convert = "cellpack.bin.simularium_converter:main" +pack = "cellpack.bin.pack:main" +upload = "cellpack.bin.upload:main" + +[tool.pdm.dev-dependencies] setup = [ "pytest-runner>=5.2", ] test = [ - "black>=19.10b0, <=23.0", - "flake8-debugger>=3.2.1", - "flake8>=3.8.3, <=6.0.0", "pytest-cov>=2.9.0", "pytest-raises>=0.11", "pytest>=5.4.3", ] -dev = [ - "Sphinx>=3.4.3", - "aicsimageio>=4.10.0", +lint = [ "black>=19.10b0, <=23.0", - "bump2version>=1.0.1", - "coverage>=5.1", "flake8-debugger>=3.2.1", "flake8>=3.8.3, <=6.0.0", - "ipython>=7.15.0", - "m2r2>=0.2.7", - "mdutils>=1.4.0", - "pandas>=1.2.4", - "pytest-cov>=2.9.0", - "pytest-raises>=0.11", - "pytest-runner>=5.2", - "pytest-runner>=5.2", - "pytest>=5.4.3", - "scikit-learn>=1.1.3", - "seaborn>=0.12.1", - "sphinx_rtd_theme>=0.5.1", - "tox>=3.15.2", - "tqdm>=4.64.1", - "twine>=3.1.1", - "wheel>=0.34.2", ] -all = [ +dev = [ "Sphinx>=3.4.3", - "aicsimageio>=4.10.0", - "aicsimageio>=4.10.0", - "black>=19.10b0, <=23.0", - "boto3>=1.28.3", 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"cellpack.bin.upload:main" +[tool.pdm.scripts] +requirements = "pdm export -f requirements --without-hashes -o" [build-system] requires = ["pdm-backend"] -build-backend = "pdm.backend" +build-backend = "pdm.backend" \ No newline at end of file From 65fd2272ec86a069e5196f1e814922918f957f23 Mon Sep 17 00:00:00 2001 From: Saurabh Mogre Date: Thu, 17 Oct 2024 12:16:28 -0700 Subject: [PATCH 13/21] Update requirements files --- requirements/linux/requirements.txt | 2074 +++---------------------- requirements/macos/requirements.txt | 2074 +++---------------------- requirements/windows/requirements.txt | 2074 +++---------------------- 3 files changed, 570 insertions(+), 5652 deletions(-) diff --git a/requirements/linux/requirements.txt b/requirements/linux/requirements.txt index 9b163779..b5646963 100644 --- a/requirements/linux/requirements.txt +++ b/requirements/linux/requirements.txt @@ -1,1887 +1,193 @@ # This file is @generated by PDM. # Please do not edit it manually. 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--hash=sha256:e4ca3b9f370f218cc2a0309542cab8d0acdfd66667e7c37d04d617012485f904 \ - --hash=sha256:e4ee8b8639070ff246ad3649294336b06db37a94bdea0d09ea491603e0be73b8 \ - --hash=sha256:e52f77a0cd246086afde8815039f3e16f8d2be51786c0a39b57104c563c5cbb0 \ - --hash=sha256:eaea112aed589131f73d50d570a6864728bd7c0c66ef6c9154ed7b59f24da611 \ - --hash=sha256:ed20a4bdc635f36cb19e630bfc644181dd075839b6fc84cac51c0f381ac472e2 \ - --hash=sha256:eedc3f247ee7b3808ea07205f3e7d7879bc19ad3e6222195cd5fbf9988853e4d \ - --hash=sha256:f0e1844ad47c7bd5d6fa784f1d4accc5f4168b48999303a868fe0f8597bde715 \ - --hash=sha256:f4fe99ce44128c71233d0d72152db31ca119711dfc5f2c82385ad611d8d7f897 \ - --hash=sha256:f8cfd847e6b9ecf9f2f2531c8427035f291ec286c0a4944b0a9fce58c6446046 \ - --hash=sha256:f9ca0e6ce7774dc7830dc0cc4bb6b3eec769db667f230e7c770a628c1aa5681b \ - --hash=sha256:fa2bea05ff0a8fb4d8124498e00e02398f06d23cdadd0fe027d84a3f7afde31e \ - --hash=sha256:fbda058a9a68bec347962595f50546a8a4a34fd7b0654a7b9697917dc2bf810d \ - --hash=sha256:ffd591e22b22f9cb48e472529db6a47203c41c2c5911ff0a52e85723196c0d75 -zarr==2.15.0 \ - --hash=sha256:3894001c0bb5d68d3d21a0562cc49e6ba14fee7d17ad2be8d088ab301665a4c6 \ - --hash=sha256:7296b9f42cdc9096c5349527e71492c1b05ed5464027bfa5d008339796d00b9f -zict==3.0.0 \ - --hash=sha256:5796e36bd0e0cc8cf0fbc1ace6a68912611c1dbd74750a3f3026b9b9d6a327ae \ - --hash=sha256:e321e263b6a97aafc0790c3cfb3c04656b7066e6738c37fffcca95d803c9fba5 -zipp==3.20.2; python_version < "3.12" \ - --hash=sha256:a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350 \ - --hash=sha256:bc9eb26f4506fda01b81bcde0ca78103b6e62f991b381fec825435c836edbc29 +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/requirements/macos/requirements.txt b/requirements/macos/requirements.txt index 9b163779..b5646963 100644 --- a/requirements/macos/requirements.txt +++ b/requirements/macos/requirements.txt @@ -1,1887 +1,193 @@ # This file is 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+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 index 9b163779..b5646963 100644 --- a/requirements/windows/requirements.txt +++ b/requirements/windows/requirements.txt @@ -1,1887 +1,193 @@ # This file is @generated by PDM. # Please do not edit it manually. -aicsimageio==4.14.0 \ - --hash=sha256:0f6684587b1d833ce5b10f3e81314e2a89269cd94bd09747fcd6460f3119855c \ - --hash=sha256:b3df2beba7d000c35660816116d562bfe96ed2beb79713b023a7579e5e72c646 -aiohappyeyeballs==2.4.3 \ - --hash=sha256:75cf88a15106a5002a8eb1dab212525c00d1f4c0fa96e551c9fbe6f09a621586 \ - --hash=sha256:8a7a83727b2756f394ab2895ea0765a0a8c475e3c71e98d43d76f22b4b435572 -aiohttp==3.10.10 \ - 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--hash=sha256:eedc3f247ee7b3808ea07205f3e7d7879bc19ad3e6222195cd5fbf9988853e4d \ - --hash=sha256:f0e1844ad47c7bd5d6fa784f1d4accc5f4168b48999303a868fe0f8597bde715 \ - --hash=sha256:f4fe99ce44128c71233d0d72152db31ca119711dfc5f2c82385ad611d8d7f897 \ - --hash=sha256:f8cfd847e6b9ecf9f2f2531c8427035f291ec286c0a4944b0a9fce58c6446046 \ - --hash=sha256:f9ca0e6ce7774dc7830dc0cc4bb6b3eec769db667f230e7c770a628c1aa5681b \ - --hash=sha256:fa2bea05ff0a8fb4d8124498e00e02398f06d23cdadd0fe027d84a3f7afde31e \ - --hash=sha256:fbda058a9a68bec347962595f50546a8a4a34fd7b0654a7b9697917dc2bf810d \ - --hash=sha256:ffd591e22b22f9cb48e472529db6a47203c41c2c5911ff0a52e85723196c0d75 -zarr==2.15.0 \ - --hash=sha256:3894001c0bb5d68d3d21a0562cc49e6ba14fee7d17ad2be8d088ab301665a4c6 \ - --hash=sha256:7296b9f42cdc9096c5349527e71492c1b05ed5464027bfa5d008339796d00b9f -zict==3.0.0 \ - --hash=sha256:5796e36bd0e0cc8cf0fbc1ace6a68912611c1dbd74750a3f3026b9b9d6a327ae \ - --hash=sha256:e321e263b6a97aafc0790c3cfb3c04656b7066e6738c37fffcca95d803c9fba5 -zipp==3.20.2; python_version < "3.12" \ - --hash=sha256:a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350 \ - --hash=sha256:bc9eb26f4506fda01b81bcde0ca78103b6e62f991b381fec825435c836edbc29 +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" From f736068a0b63893d68dd00a80c758600754e4c9b Mon Sep 17 00:00:00 2001 From: Saurabh Mogre Date: Thu, 17 Oct 2024 12:49:04 -0700 Subject: [PATCH 14/21] Update dependency installation script --- .github/actions/dependencies/action.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/actions/dependencies/action.yml b/.github/actions/dependencies/action.yml index 7016a94e..38837992 100644 --- a/.github/actions/dependencies/action.yml +++ b/.github/actions/dependencies/action.yml @@ -8,4 +8,5 @@ runs: - 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 + run: pdm sync -d --only-keep + run: source .venv/bin/activate \ No newline at end of file From 8c6d199964096de2304c6ec1c8a0db4d1f303b44 Mon Sep 17 00:00:00 2001 From: Saurabh Mogre Date: Thu, 17 Oct 2024 13:02:27 -0700 Subject: [PATCH 15/21] Activate environment after installing dependencies --- .github/actions/dependencies/action.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/actions/dependencies/action.yml b/.github/actions/dependencies/action.yml index 38837992..1ba22ec5 100644 --- a/.github/actions/dependencies/action.yml +++ b/.github/actions/dependencies/action.yml @@ -8,5 +8,6 @@ runs: - name: Install dependencies shell: bash # --only-keep flag in case the environment is restored from a stale cache. - run: pdm sync -d --only-keep - run: source .venv/bin/activate \ No newline at end of file + run: | + pdm sync -d --only-keep + source .venv/bin/activate \ No newline at end of file From 921738be8feb9da70a8b466a2c415e9061211b6d Mon Sep 17 00:00:00 2001 From: Saurabh Mogre Date: Thu, 17 Oct 2024 14:18:33 -0700 Subject: [PATCH 16/21] Run workflows through pdm --- .github/workflows/analyze.yml | 5 ++--- .github/workflows/ci.yml | 6 +++--- .github/workflows/cleanup-firebase.yml | 2 +- 3 files changed, 6 insertions(+), 7 deletions(-) diff --git a/.github/workflows/analyze.yml b/.github/workflows/analyze.yml index 184e7239..3537043c 100644 --- a/.github/workflows/analyze.yml +++ b/.github/workflows/analyze.yml @@ -18,15 +18,14 @@ jobs: - uses: actions/checkout@v4 - uses: ./.github/actions/dependencies - name: Pack test recipe - shell: bash 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@v4 with: diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index cfbe2046..37fc88d5 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -34,7 +34,7 @@ jobs: - 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 @@ -46,10 +46,10 @@ jobs: - 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/') diff --git a/.github/workflows/cleanup-firebase.yml b/.github/workflows/cleanup-firebase.yml index 4bbebb94..4ba7a84d 100644 --- a/.github/workflows/cleanup-firebase.yml +++ b/.github/workflows/cleanup-firebase.yml @@ -19,4 +19,4 @@ jobs: FIREBASE_TOKEN: ${{ secrets.FIREBASE_TOKEN }} FIREBASE_EMAIL: ${{ secrets.FIREBASE_EMAIL }} run: | - python cellpack/bin/cleanup_tasks.py + pdm run python cellpack/bin/cleanup_tasks.py From be7bf177895651764147732affc491dde396f8f6 Mon Sep 17 00:00:00 2001 From: Saurabh Mogre Date: Thu, 17 Oct 2024 14:26:27 -0700 Subject: [PATCH 17/21] Remove venv activation specific to linux --- .github/actions/dependencies/action.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/actions/dependencies/action.yml b/.github/actions/dependencies/action.yml index 1ba22ec5..69e80abe 100644 --- a/.github/actions/dependencies/action.yml +++ b/.github/actions/dependencies/action.yml @@ -9,5 +9,4 @@ runs: shell: bash # --only-keep flag in case the environment is restored from a stale cache. run: | - pdm sync -d --only-keep - source .venv/bin/activate \ No newline at end of file + pdm sync -d --only-keep \ No newline at end of file From 0ea3062fb97606b37c998776f748ce21f500f44c Mon Sep 17 00:00:00 2001 From: Saurabh Mogre Date: Thu, 17 Oct 2024 14:26:44 -0700 Subject: [PATCH 18/21] Update cml setup version --- .github/workflows/analyze.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/analyze.yml b/.github/workflows/analyze.yml index 3537043c..79b1fedf 100644 --- a/.github/workflows/analyze.yml +++ b/.github/workflows/analyze.yml @@ -53,7 +53,7 @@ jobs: - uses: actions/download-artifact@v4 - name: Copy files to results bucket run: aws s3 cp ./results s3://cellpack-results/${{ 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: From 479374f76f5092a5c58495e8dd01020c1bfc842c Mon Sep 17 00:00:00 2001 From: Saurabh Mogre Date: Thu, 17 Oct 2024 15:29:43 -0700 Subject: [PATCH 19/21] Update black version --- docs/pdm.md | 2 +- pdm.lock | 57 +++++++++++++++++++++++++------------------------- pyproject.toml | 5 ++++- 3 files changed, 34 insertions(+), 30 deletions(-) diff --git a/docs/pdm.md b/docs/pdm.md index 5bb4506d..b9b43b72 100644 --- a/docs/pdm.md +++ b/docs/pdm.md @@ -27,4 +27,4 @@ pdm update {package-name} 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 [like this one](https://github.com/aics-int/nuc-morph-analysis/pull/124) to update all three `requirements/{platform}/requirements.txt` files based on your changes. This second PR must be merged before any further changes are made to `pdm.lock`. \ No newline at end of file +7. A Github action will make a second pull request to update all three `requirements/{platform}/requirements.txt` files based on your changes. This second PR must be merged before any further changes are made to `pdm.lock`. \ No newline at end of file diff --git a/pdm.lock b/pdm.lock index 7293795b..4ad7aa9e 100644 --- a/pdm.lock +++ b/pdm.lock @@ -5,7 +5,7 @@ groups = ["default", "dev", "lint", "setup", "test"] strategy = ["inherit_metadata"] lock_version = "4.5.0" -content_hash = "sha256:1097f7223c5fa5eb81c6627d1c6b1515ae527f10eff1487c26b1b9477ae3c1ae" +content_hash = "sha256:1495b5a1714491f6b8403215e288c657f5bb75be7928c1489da5032b3b66570d" [[metadata.targets]] requires_python = "==3.9.*" @@ -199,45 +199,47 @@ files = [ [[package]] name = "black" -version = "22.12.0" -requires_python = ">=3.7" +version = "24.8.0" +requires_python = ">=3.8" summary = "The uncompromising code formatter." groups = ["lint"] dependencies = [ "click>=8.0.0", "mypy-extensions>=0.4.3", + "packaging>=22.0", "pathspec>=0.9.0", "platformdirs>=2", - "tomli>=1.1.0; python_full_version < \"3.11.0a7\"", - "typed-ast>=1.4.2; python_version < \"3.8\" and implementation_name == \"cpython\"", - 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"botocore<1.36.0,>=1.35.42", + "botocore<1.36.0,>=1.35.43", "jmespath<2.0.0,>=0.7.1", "s3transfer<0.11.0,>=0.10.0", ] files = [ - {file = "boto3-1.35.42-py3-none-any.whl", hash = "sha256:e1f36f8be453505cebcc3da178ea081b2a06c0e5e1cdee774f1067599b8d9c3e"}, - {file = "boto3-1.35.42.tar.gz", hash = "sha256:a5b00f8b82dce62870759f04861747944da834d64a64355970120c475efdafc0"}, + {file = "boto3-1.35.43-py3-none-any.whl", hash = "sha256:e6a50a0599f75b21de0de1a551a0564793d25b304fa623e4052e527b268de734"}, + {file = "boto3-1.35.43.tar.gz", hash = "sha256:0197f460632804577aa78b2f6daf7b823bffa9d4d67a5cebb179efff0fe9631b"}, ] [[package]] name = "botocore" -version = "1.35.42" +version = "1.35.43" requires_python = ">=3.8" summary = "Low-level, data-driven core of boto 3." groups = ["default"] @@ -248,8 +250,8 @@ dependencies = [ "urllib3<1.27,>=1.25.4; python_version < \"3.10\"", ] files = [ - {file = "botocore-1.35.42-py3-none-any.whl", hash = "sha256:05af0bb8b9cea7ce7bc589c332348d338a21b784e9d088a588fd10ec145007ff"}, - {file = "botocore-1.35.42.tar.gz", hash = "sha256:af348636f73dc24b7e2dc760a34d08c8f2f94366e9b4c78d877307b128abecef"}, + {file = "botocore-1.35.43-py3-none-any.whl", hash = "sha256:7cfdee9117617da97daaf259dd8484bcdc259c59eb7d1ce7db9ecf8506b7d36c"}, + {file = "botocore-1.35.43.tar.gz", hash = "sha256:04539b85ade060601a3023cacb538fc17aad8c059a5a2e18fe4bc5d0d91fbd72"}, ] [[package]] @@ -1440,7 +1442,6 @@ files = [ [[package]] name = "mdutils" version = "1.6.0" -requires_python = "<4.0,>=3.6" summary = "Useful package for creating Markdown files while executing python code." groups = ["default"] files = [ @@ -1648,7 +1649,7 @@ name = "packaging" version = "24.1" requires_python = ">=3.8" summary = "Core utilities for Python packages" -groups = ["default", "dev", "test"] +groups = ["default", "dev", "lint", "test"] files = [ {file = "packaging-24.1-py3-none-any.whl", hash = "sha256:5b8f2217dbdbd2f7f384c41c628544e6d52f2d0f53c6d0c3ea61aa5d1d7ff124"}, {file = "packaging-24.1.tar.gz", hash = "sha256:026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002"}, @@ -1882,19 +1883,19 @@ files = [ [[package]] name = "psutil" -version = "6.0.0" +version = "6.1.0" requires_python = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" summary = "Cross-platform lib for process and system monitoring in Python." groups = ["default"] files = [ - 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"black>=19.10b0, <=23.0", + "black>=19.10b0, <=24.8.0", "flake8-debugger>=3.2.1", "flake8>=3.8.3, <=6.0.0", ] @@ -79,6 +79,9 @@ dev = [ [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 From 5c690d34a6bce9adc13a52d6aec7834f4a367e49 Mon Sep 17 00:00:00 2001 From: Saurabh Mogre Date: Thu, 17 Oct 2024 15:29:52 -0700 Subject: [PATCH 20/21] Formatting changes --- cellpack/autopack/Graphics.py | 10 +++++----- cellpack/autopack/ingredient/grow.py | 4 ++-- cellpack/autopack/upy/hostHelper.py | 24 ++++++++++++------------ 3 files changed, 19 insertions(+), 19 deletions(-) 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: From 58e4e55bbbc21de1956316fcc64c91e972fb51be Mon Sep 17 00:00:00 2001 From: Saurabh Mogre Date: Fri, 22 Nov 2024 15:22:59 -0800 Subject: [PATCH 21/21] * Add command "clean" to pyproject.toml * Update makefile to move cleanup * Specify base python in tox.ini --- Makefile | 10 +++++----- pyproject.toml | 1 + tox.ini | 1 + 3 files changed, 7 insertions(+), 5 deletions(-) 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/pyproject.toml b/pyproject.toml index 67e9dafc..7c17217a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -49,6 +49,7 @@ 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 = [ diff --git a/tox.ini b/tox.ini index 64effe1c..0efa77d2 100644 --- a/tox.ini +++ b/tox.ini @@ -1,5 +1,6 @@ [tox] env_list = py39, lint +base_python = python3.9 [testenv:lint] groups = lint