From 4fd54c3b52bb6b6f852d9453b7c0f57df44b7e8c Mon Sep 17 00:00:00 2001 From: Ruge Li Date: Wed, 8 May 2024 11:14:43 -0700 Subject: [PATCH 01/17] test --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index a080c60d..b0d724f6 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -89,5 +89,5 @@ jobs: run: | python setup.py sdist bdist_wheel - name: Publish to PyPI - uses: pypa/gh-action-pypi-publish@release/v1 + uses: pypa/gh-action-pypi-publish@release/v1 From d258127d0155b5db973fc463e95a91b25b843504 Mon Sep 17 00:00:00 2001 From: Ruge Li Date: Wed, 8 May 2024 11:28:26 -0700 Subject: [PATCH 02/17] option 1: using multiple python versions --- .github/workflows/ci.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b0d724f6..f3aae441 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -26,13 +26,13 @@ jobs: runs-on: ${{ matrix.os }} strategy: matrix: - python-version: [3.9] + python-version: ["3.9", "3.10", "3.11", "3.12"] os: [ubuntu-latest, windows-latest, macOS-latest] steps: - - uses: actions/checkout@v1 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v1 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Install Dependencies @@ -80,7 +80,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v1 with: - python-version: 3.9 + python-version: "3.x" - name: Install Dependencies run: | python -m pip install --upgrade pip From 2ce30849561ba6b5651b826c6cbbde7a359576e7 Mon Sep 17 00:00:00 2001 From: Ruge Li Date: Wed, 8 May 2024 11:44:20 -0700 Subject: [PATCH 03/17] option 2: using a specific python version --- .github/workflows/ci.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index f3aae441..45e3219c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -3,7 +3,7 @@ name: Continuous Integration on: push: branches: - - main + - update/python_version tags: - "v*" pull_request: @@ -26,7 +26,7 @@ jobs: runs-on: ${{ matrix.os }} strategy: matrix: - python-version: ["3.9", "3.10", "3.11", "3.12"] + python-version: ["3.x"] os: [ubuntu-latest, windows-latest, macOS-latest] steps: From 1849826ab75eacaa42d490307e0b187058f7103c Mon Sep 17 00:00:00 2001 From: Ruge Li Date: Wed, 8 May 2024 11:56:36 -0700 Subject: [PATCH 04/17] update numpy version --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 10729b39..19e42963 100644 --- a/setup.py +++ b/setup.py @@ -53,7 +53,7 @@ "fire>=0.4.0", "firebase_admin>=6.0.1", "matplotlib>=3.3.4", - "numpy>=1.19.2", + "numpy>=1.26.4", "pmw==2.0.1", "scipy>=1.6.2", "simulariumio>=1.6.3", From a8c1a55e90e06367659fa83429684b95bbd470f4 Mon Sep 17 00:00:00 2001 From: Ruge Li Date: Wed, 8 May 2024 12:04:11 -0700 Subject: [PATCH 05/17] downgrade python version to 3.11 for lint and pytest --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 45e3219c..d031c694 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -53,7 +53,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v5 with: - python-version: 3.9 + python-version: 3.11 - name: Install Dependencies run: | python -m pip install --upgrade pip From 3e5a3394e99c7764c0d503ee6fe4cbe093682151 Mon Sep 17 00:00:00 2001 From: Ruge Li Date: Wed, 8 May 2024 12:15:46 -0700 Subject: [PATCH 06/17] use a stable version 3.11 --- .github/workflows/ci.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index d031c694..1e0e8600 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -26,7 +26,7 @@ jobs: runs-on: ${{ matrix.os }} strategy: matrix: - python-version: ["3.x"] + python-version: [3.11] os: [ubuntu-latest, windows-latest, macOS-latest] steps: @@ -80,7 +80,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v1 with: - python-version: "3.x" + python-version: 3.11 - name: Install Dependencies run: | python -m pip install --upgrade pip From 0802ddfa335affb4e8ad9ffe6a321281e171fe76 Mon Sep 17 00:00:00 2001 From: Ruge Li Date: Wed, 8 May 2024 12:26:08 -0700 Subject: [PATCH 07/17] use 3.10 --- .github/workflows/ci.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 1e0e8600..7c4ffd6f 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -26,7 +26,7 @@ jobs: runs-on: ${{ matrix.os }} strategy: matrix: - python-version: [3.11] + python-version: [3.10] os: [ubuntu-latest, windows-latest, macOS-latest] steps: @@ -53,7 +53,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v5 with: - python-version: 3.11 + python-version: 3.10 - name: Install Dependencies run: | python -m pip install --upgrade pip @@ -80,7 +80,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v1 with: - python-version: 3.11 + python-version: 3.10 - name: Install Dependencies run: | python -m pip install --upgrade pip From b2269e48fdfa36c975581103990001cc10cb3c09 Mon Sep 17 00:00:00 2001 From: Ruge Li Date: Wed, 8 May 2024 12:28:58 -0700 Subject: [PATCH 08/17] use "3.10" --- .github/workflows/ci.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 7c4ffd6f..cb274956 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -26,7 +26,7 @@ jobs: runs-on: ${{ matrix.os }} strategy: matrix: - python-version: [3.10] + python-version: ["3.10"] os: [ubuntu-latest, windows-latest, macOS-latest] steps: @@ -53,7 +53,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v5 with: - python-version: 3.10 + python-version: "3.10" - name: Install Dependencies run: | python -m pip install --upgrade pip @@ -80,7 +80,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v1 with: - python-version: 3.10 + python-version: "3.10" - name: Install Dependencies run: | python -m pip install --upgrade pip @@ -89,5 +89,5 @@ jobs: run: | python setup.py sdist bdist_wheel - name: Publish to PyPI - uses: pypa/gh-action-pypi-publish@release/v1 + uses: pypa/gh-action-pypi-publish@release/v1 From 0bbe81c3f605ed0c45a8b743fc6e9b7f72ea068a Mon Sep 17 00:00:00 2001 From: Ruge Li Date: Wed, 8 May 2024 12:35:13 -0700 Subject: [PATCH 09/17] switch testing branch to main --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index cb274956..5e59d4f0 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -3,7 +3,7 @@ name: Continuous Integration on: push: branches: - - update/python_version + - main tags: - "v*" pull_request: From e7ffdf7338da7b97704e16a3382ea052f0e85981 Mon Sep 17 00:00:00 2001 From: Ruge Li Date: Thu, 9 May 2024 14:39:55 -0700 Subject: [PATCH 10/17] test: update setup-python --- .github/workflows/ci.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 5e59d4f0..9c8ffd7a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -26,7 +26,7 @@ jobs: runs-on: ${{ matrix.os }} strategy: matrix: - python-version: ["3.10"] + python-version: [3.9] os: [ubuntu-latest, windows-latest, macOS-latest] steps: @@ -53,7 +53,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v5 with: - python-version: "3.10" + python-version: 3.9 - name: Install Dependencies run: | python -m pip install --upgrade pip @@ -76,11 +76,11 @@ jobs: id-token: write steps: - - uses: actions/checkout@v1 + - uses: actions/checkout@v4 - name: Set up Python - uses: actions/setup-python@v1 + uses: actions/setup-python@v5 with: - python-version: "3.10" + python-version: 3.9 - name: Install Dependencies run: | python -m pip install --upgrade pip From eb1df432a6cddf4a994a85ea9e89fba57caec330 Mon Sep 17 00:00:00 2001 From: Ruge Li Date: Thu, 9 May 2024 14:54:44 -0700 Subject: [PATCH 11/17] revert numpy version --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 19e42963..10729b39 100644 --- a/setup.py +++ b/setup.py @@ -53,7 +53,7 @@ "fire>=0.4.0", "firebase_admin>=6.0.1", "matplotlib>=3.3.4", - "numpy>=1.26.4", + "numpy>=1.19.2", "pmw==2.0.1", "scipy>=1.6.2", "simulariumio>=1.6.3", From ee2195f1425f288c817fcbd244ac16e9b4987267 Mon Sep 17 00:00:00 2001 From: Saurabh Mogre Date: Thu, 9 May 2024 15:33:11 -0700 Subject: [PATCH 12/17] Cache installed python dependencies --- .github/workflows/ci.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 9c8ffd7a..593285d9 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -35,6 +35,7 @@ jobs: uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} + cache: "pip" - name: Install Dependencies run: | python -m pip install --upgrade pip @@ -54,6 +55,7 @@ jobs: uses: actions/setup-python@v5 with: python-version: 3.9 + cache: "pip" - name: Install Dependencies run: | python -m pip install --upgrade pip @@ -81,6 +83,7 @@ jobs: uses: actions/setup-python@v5 with: python-version: 3.9 + cache: "pip" - name: Install Dependencies run: | python -m pip install --upgrade pip From 747cdab4a5dca2edac14197308a3aaa63eb7aaf9 Mon Sep 17 00:00:00 2001 From: Saurabh Mogre Date: Thu, 9 May 2024 15:37:00 -0700 Subject: [PATCH 13/17] Update Python setup action and add pip caching --- .github/workflows/build-docs.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml index c4388350..70105215 100644 --- a/.github/workflows/build-docs.yml +++ b/.github/workflows/build-docs.yml @@ -14,9 +14,10 @@ jobs: with: persist-credentials: false - name: Set up Python - uses: actions/setup-python@v1 + uses: actions/setup-python@v5 with: python-version: 3.9 + cache: "pip" - name: Install Dependencies run: | pip install --upgrade pip From 5c712472a5d738dc04760b0af76057e6d4821c6c Mon Sep 17 00:00:00 2001 From: Saurabh Mogre Date: Thu, 9 May 2024 15:37:17 -0700 Subject: [PATCH 14/17] Add pip caching to setup-python action in analyze.yml --- .github/workflows/analyze.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/analyze.yml b/.github/workflows/analyze.yml index 0333e708..99c02aaf 100644 --- a/.github/workflows/analyze.yml +++ b/.github/workflows/analyze.yml @@ -20,6 +20,7 @@ jobs: uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} + cache: "pip" - name: Install Dependencies run: | python -m pip install --upgrade pip From ec53c853e0ec4b269ae89c69b62525dccd8315b9 Mon Sep 17 00:00:00 2001 From: Saurabh Mogre Date: Thu, 9 May 2024 16:04:27 -0700 Subject: [PATCH 15/17] Remove duplicate mdutils from analysis_requirements --- setup.py | 1 - 1 file changed, 1 deletion(-) diff --git a/setup.py b/setup.py index 10729b39..ed27ac0f 100644 --- a/setup.py +++ b/setup.py @@ -28,7 +28,6 @@ "seaborn>=0.12.1", "aicsimageio>=4.10.0", "pandas>=1.2.4", - "mdutils>=1.4.0", ] dev_requirements = [ From c91b8c2b5c6d6f99dc85b553df6b33bba8c28029 Mon Sep 17 00:00:00 2001 From: Saurabh Mogre Date: Thu, 9 May 2024 16:04:53 -0700 Subject: [PATCH 16/17] add pyproject.toml --- pyproject.toml | 144 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 144 insertions(+) create mode 100644 pyproject.toml diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 00000000..1a3bcea8 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,144 @@ +[tool.pdm] + +[project] +name = "cellpack" +version = "1.0.8" +description = "algorithm to pack molecular recipes" +keywords = ["cellpack"] +readme = "README.md" +authors = [ + {name = "Megan Riel-Mehan", 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", +] +requires-python = ">=3.8" +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", + "pandas>=1.2.4", + "plotly>=5.3.1", + "pmw==2.0.1", + "pycollada==0.7.2", + "pyembree>=0.1.8", + "pymunk>=6.2.0", + "python-dotenv>=1.0.0", + "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.optional-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", + "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 = [ + "Sphinx>=3.4.3", + "aicsimageio>=4.10.0", + "aicsimageio>=4.10.0", + "black>=19.10b0, <=23.0", + "boto3>=1.28.3", + "bump2version>=1.0.1", + "coverage>=5.1", + "deepdiff>=5.5.0", + "fire>=0.4.0", + "firebase_admin>=6.0.1", + "flake8-debugger>=3.2.1", + "flake8>=3.8.3, <=6.0.0", + "ipython>=7.15.0", + "m2r2>=0.2.7", + "matplotlib>=3.3.4", + "mdutils>=1.4.0", + "mdutils>=1.4.0", + "moto>=5.0.2", + "numpy>=1.19.2", + "pandas>=1.2.4", + "pandas>=1.2.4", + "plotly>=5.3.1", + "pmw==2.0.1", + "pycollada==0.7.2", + "pyembree>=0.1.8", + "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", + "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 efe8c99cbdd3f45127ddc984644ce77ef5cbf838 Mon Sep 17 00:00:00 2001 From: Saurabh Mogre Date: Mon, 13 May 2024 13:42:37 -0700 Subject: [PATCH 17/17] Specify setup.py as cache dependency path --- .github/workflows/analyze.yml | 1 + .github/workflows/build-docs.yml | 1 + .github/workflows/ci.yml | 3 + pyproject.toml | 144 ------------------------------- 4 files changed, 5 insertions(+), 144 deletions(-) delete mode 100644 pyproject.toml diff --git a/.github/workflows/analyze.yml b/.github/workflows/analyze.yml index 99c02aaf..d34cb5b5 100644 --- a/.github/workflows/analyze.yml +++ b/.github/workflows/analyze.yml @@ -21,6 +21,7 @@ jobs: with: python-version: ${{ matrix.python-version }} cache: "pip" + cache-dependency-path: setup.py - name: Install Dependencies run: | python -m pip install --upgrade pip diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml index 70105215..cbfa999b 100644 --- a/.github/workflows/build-docs.yml +++ b/.github/workflows/build-docs.yml @@ -18,6 +18,7 @@ jobs: with: python-version: 3.9 cache: "pip" + cache-dependency-path: setup.py - name: Install Dependencies run: | pip install --upgrade pip diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 593285d9..78278c7d 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -36,6 +36,7 @@ jobs: with: python-version: ${{ matrix.python-version }} cache: "pip" + cache-dependency-path: setup.py - name: Install Dependencies run: | python -m pip install --upgrade pip @@ -56,6 +57,7 @@ jobs: with: python-version: 3.9 cache: "pip" + cache-dependency-path: setup.py - name: Install Dependencies run: | python -m pip install --upgrade pip @@ -84,6 +86,7 @@ jobs: with: python-version: 3.9 cache: "pip" + cache-dependency-path: setup.py - name: Install Dependencies run: | python -m pip install --upgrade pip diff --git a/pyproject.toml b/pyproject.toml deleted file mode 100644 index 1a3bcea8..00000000 --- a/pyproject.toml +++ /dev/null @@ -1,144 +0,0 @@ -[tool.pdm] - -[project] -name = "cellpack" -version = "1.0.8" -description = "algorithm to pack molecular recipes" -keywords = ["cellpack"] -readme = "README.md" -authors = [ - {name = "Megan Riel-Mehan", 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", -] -requires-python = ">=3.8" -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", - "pandas>=1.2.4", - "plotly>=5.3.1", - "pmw==2.0.1", - "pycollada==0.7.2", - "pyembree>=0.1.8", - "pymunk>=6.2.0", - "python-dotenv>=1.0.0", - "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.optional-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", - "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 = [ - "Sphinx>=3.4.3", - "aicsimageio>=4.10.0", - "aicsimageio>=4.10.0", - "black>=19.10b0, <=23.0", - "boto3>=1.28.3", - "bump2version>=1.0.1", - "coverage>=5.1", - "deepdiff>=5.5.0", - "fire>=0.4.0", - "firebase_admin>=6.0.1", - "flake8-debugger>=3.2.1", - "flake8>=3.8.3, <=6.0.0", - "ipython>=7.15.0", - "m2r2>=0.2.7", - "matplotlib>=3.3.4", - "mdutils>=1.4.0", - "mdutils>=1.4.0", - "moto>=5.0.2", - "numpy>=1.19.2", - "pandas>=1.2.4", - "pandas>=1.2.4", - "plotly>=5.3.1", - "pmw==2.0.1", - "pycollada==0.7.2", - "pyembree>=0.1.8", - "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", - "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", - 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