Reduce number of files listing deps (#154)

* Reduce number of files listing deps

* Install cython before anything else

* Fix missing deps before install

* Fix typo in setup.cfg extra option

* Add Read the Docs config file

* nbmake only used for testing docs, not building docs

.github/workflows/docs.yaml

@@ -1,3 +1,5 @@
+# TODO: it should be possible to test documentation builds directly on Read the Docs:
+# https://docs.readthedocs.io/en/stable/pull-requests.html
 name: docs
 on:
   push:
@@ -17,8 +19,8 @@ jobs:
       uses: actions/setup-python@v2
       with:
         python-version: 3.9
-    - name: Install pydocstyle
-      run: pip install 'pydocstyle[toml]>=6.1'
+    - name: Install pip dependencies
+      run: pip install .[style]
     - name: Run pydocstyle checks
       run: pydocstyle
   sphinx:
@@ -35,7 +37,7 @@ jobs:
       run: sudo apt-get install pandoc
     - name: Install pip dependencies
       run: |
-        pip install cython numpy  # needed for pycocotools
-        pip install -r requirements.txt
+        pip install .[train]
+        pip install -r docs/requirements.txt
     - name: Run sphinx checks
       run: cd docs && make html

.github/workflows/release.yaml

@@ -18,10 +18,7 @@ jobs:
       with:
         python-version: 3.9
     - name: Install pip dependencies
-      run: |
-        pip install cython numpy  # needed for pycocotools
-        pip install -r requirements.txt
-        pip list
+      run: pip install .[tests]
     - name: Run notebook checks
       run: pytest --nbmake docs/tutorials
   integration:
@@ -35,9 +32,6 @@ jobs:
       with:
         python-version: 3.9
     - name: Install pip dependencies
-      run: |
-        pip install cython numpy  # needed for pycocotools
-        pip install -r requirements.txt
-        pip list
+      run: pip install .[tests]
     - name: Run integration checks
       run: pytest -m slow

.github/workflows/style.yaml

@@ -17,8 +17,8 @@ jobs:
       uses: actions/setup-python@v2
       with:
         python-version: 3.9
-    - name: Install black
-      run: pip install 'black>=21.4b0'
+    - name: Install pip dependencies
+      run: pip install .[style]
     - name: Run black checks
       run: black . --check --diff
   flake8:
@@ -31,8 +31,8 @@ jobs:
       uses: actions/setup-python@v2
       with:
         python-version: 3.9
-    - name: Install flake8
-      run: pip install 'flake8>=3.8'
+    - name: Install pip dependencies
+      run: pip install .[style]
     - name: Run flake8 checks
       run: flake8
   isort:
@@ -45,7 +45,7 @@ jobs:
       uses: actions/setup-python@v2
       with:
         python-version: 3.9
-    - name: Install isort
-      run: pip install 'isort[colors]>=5.8'
+    - name: Install pip dependencies
+      run: pip install .[style]
     - name: Run isort checks
       run: isort . --check --diff

.github/workflows/tests.yaml

@@ -17,10 +17,10 @@ jobs:
       uses: actions/setup-python@v2
       with:
         python-version: 3.9
-    - name: Install dependencies
+    - name: Install pip dependencies
       run: |
         pip install cython numpy  # needed for pycocotools
-        pip install -r requirements.txt
+        pip install .[datasets,tests,train]
     - name: Run mypy checks
       run: mypy .
   pytest:
@@ -62,8 +62,7 @@ jobs:
     - name: Install pip dependencies
       run: |
         pip install cython numpy  # needed for pycocotools
-        pip install -r requirements.txt
-        pip list
+        pip install .[datasets,tests,train]
     - name: Run pytest checks
       run: pytest --cov=torchgeo --cov-report=xml
     - name: Report coverage

.readthedocs.yaml

@@ -0,0 +1,19 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Configuration of the Python environment to be used
+python:
+   install:
+   - requirements: docs/requirements.txt
+   - method: pip
+     path: .
+     extra_requirements:
+     - train
+
+# Configuration for Sphinx documentation
+sphinx:
+   configuration: docs/conf.py
+   fail_on_warning: true

docs/requirements.txt

@@ -1,66 +1,8 @@
-# black 21+ required for Python 3.9 support
-black>=21.4b0
-einops
-# fiona 1.5+ required for fiona.transform module
-fiona>=1.5
-# flake8 3.8+ depends on pyflakes 2.2+, which fixes a bug with mypy error code ignores:
-# https://github.com/PyCQA/pyflakes/pull/455
-flake8>=3.8
-h5py
 # ipywidgets 7+ required for nbsphinx
 ipywidgets>=7
-# isort 5.8+ required for extend_skip option
-isort[colors]>=5.8
-jupyterlab
-matplotlib
-# mypy 0.900+ required for pyproject.toml support
-mypy>=0.900
-# nbmake 0.1+ required to fix path_source bug
-nbmake>=0.1
 # nbsphinx 0.8.5 fixes bug with nbformat attributes
 nbsphinx>=0.8.5
-numpy
-# omegaconf 2.1+ required for to_object method
-omegaconf>=2.1
-opencv-python
-# pillow 2.9+ required for height attribute
-pillow>=2.9
-pycocotools
-# pydocstyle 6.1+ required for pyproject.toml support
-pydocstyle[toml]>=6.1
-# pyproj 2.2.0+ required for CRS object, note: pyproj 3.1+ contains threadsafe Transformer and CRS implementations
-pyproj>=2.2.0
-# pytest 6+ required for pyproject.toml support
-pytest>=6
-# pytest-cov 2.4+ required for pytest --cov flags
-pytest-cov>=2.4
-# pytorch-lightning 1.3+ required for gradient_clip_algorithm argument to Trainer
-pytorch-lightning>=1.3
 # release versions missing files, must install from master
--e git+https://github.com/pytorch/pytorch_sphinx_theme#egg=pytorch_sphinx_theme
-# radiant-mlhub 0.2.1+ required for api_key bugfix:
-# https://github.com/radiantearth/radiant-mlhub/pull/48
-radiant-mlhub>=0.2.1
-# rarfile 3+ required for correct Rar file detection
-rarfile>=3
-# rasterio 1.0.16+ required for CRS support
-rasterio>=1.0.16
-# rtree 0.5+ required for 3D index support
-rtree>=0.5
-# scikit-learn 0.18+ required for sklearn.model_selection module
-scikit-learn>=0.18
-# scipy 0.9.0+ required for scipy.io.wavfile.read
-scipy>=0.9.0
-# segmentation-models-pytorch 0.2+ required for smp.losses module
-segmentation-models-pytorch>=0.2
-# setuptools 30.4+ required for options.packages.find section in setup.cfg
-setuptools>=30.4
-# shapely 1.3.0+ is required for Python 3.x
-shapely>=1.3.0
+-e git+https://github.com/pytorch/pytorch_sphinx_theme.git#egg=pytorch_sphinx_theme
 # sphinx 3+ required for autodoc_typehints = description
-sphinx>=3,!=4.1.2
-# torch 1.7+ required for typing
-torch>=1.7
-torchmetrics
-# torchvision 0.3+ required for download_file_from_google_drive
-torchvision>=0.3
+sphinx>=3

environment.yml

@@ -9,12 +9,12 @@ dependencies:
   - numpy
   - pip
   - pycocotools
-  - pyproj>=2.2.0
+  - pyproj>=2.2
   - python>=3.6
   - pytorch-gpu>=1.7
   - rarfile>=3
   - rasterio>=1.0.16
-  - shapely>=1.3.0
+  - shapely>=1.3
   - torchvision>=0.3
   - pip:
     - black>=21.4b0
@@ -36,7 +36,7 @@ dependencies:
     - radiant-mlhub>=0.2.1
     - rtree>=0.5
     - scikit-learn>=0.18
-    - scipy>=0.9.0
+    - scipy>=0.9
     - segmentation-models-pytorch>=0.2
     - setuptools>=30.4
     - sphinx>=3

requirements.txt

@@ -1,66 +0,0 @@
-# black 21+ required for Python 3.9 support
-black>=21.4b0
-einops
-# fiona 1.5+ required for fiona.transform module
-fiona>=1.5
-# flake8 3.8+ depends on pyflakes 2.2+, which fixes a bug with mypy error code ignores:
-# https://github.com/PyCQA/pyflakes/pull/455
-flake8>=3.8
-h5py
-# ipywidgets 7+ required for nbsphinx
-ipywidgets>=7
-# isort 5.8+ required for extend_skip option
-isort[colors]>=5.8
-jupyterlab
-matplotlib
-# mypy 0.900+ required for pyproject.toml support
-mypy>=0.900
-# nbmake 0.1+ required to fix path_source bug
-nbmake>=0.1
-# nbsphinx 0.8.5 fixes bug with nbformat attributes
-nbsphinx>=0.8.5
-numpy
-# omegaconf 2.1+ required for to_object method
-omegaconf>=2.1
-opencv-python
-# pillow 2.9+ required for height attribute
-pillow>=2.9
-pycocotools
-# pydocstyle 6.1+ required for pyproject.toml support
-pydocstyle[toml]>=6.1
-# pyproj 2.2.0+ required for CRS object, note: pyproj 3.1+ contains threadsafe Transformer and CRS implementations
-pyproj>=2.2.0
-# pytest 6+ required for pyproject.toml support
-pytest>=6
-# pytest-cov 2.4+ required for pytest --cov flags
-pytest-cov>=2.4
-# pytorch-lightning 1.3+ required for gradient_clip_algorithm argument to Trainer
-pytorch-lightning>=1.3
-# release versions missing files, must install from master
-git+https://github.com/pytorch/pytorch_sphinx_theme#egg=pytorch_sphinx_theme
-# radiant-mlhub 0.2.1+ required for api_key bugfix:
-# https://github.com/radiantearth/radiant-mlhub/pull/48
-radiant-mlhub>=0.2.1
-# rarfile 3+ required for correct Rar file detection
-rarfile>=3
-# rasterio 1.0.16+ required for CRS support
-rasterio>=1.0.16
-# rtree 0.5+ required for 3D index support
-rtree>=0.5
-# scikit-learn 0.18+ required for sklearn.model_selection module
-scikit-learn>=0.18
-# scipy 0.9.0+ required for scipy.io.wavfile.read
-scipy>=0.9.0
-# segmentation-models-pytorch 0.2+ required for smp.losses module
-segmentation-models-pytorch>=0.2
-# setuptools 30.4+ required for options.packages.find section in setup.cfg
-setuptools>=30.4
-# shapely 1.3.0+ is required for Python 3.x
-shapely>=1.3.0
-# sphinx 3+ required for autodoc_typehints = description
-sphinx>=3
-# torch 1.7+ required for typing
-torch>=1.7
-torchmetrics
-# torchvision 0.3+ required for download_file_from_google_drive
-torchvision>=0.3

setup.cfg

@@ -24,18 +24,27 @@ keywords = pytorch, deep learning, machine learning
 
 [options]
 setup_requires =
+    # setuptools 30.4+ required for options.packages.find section in setup.cfg
     setuptools>=30.4
 install_requires =
     einops
+    # fiona 1.5+ required for fiona.transform module
     fiona>=1.5
     matplotlib
     numpy
+    # pillow 2.9+ required for height attribute
     pillow>=2.9
-    pyproj>=2.2.0
+    # pyproj 2.2+ required for CRS object
+    pyproj>=2.2
+    # rasterio 1.0.16+ required for CRS support
     rasterio>=1.0.16
+    # rtree 0.5+ required for 3D index support
     rtree>=0.5
-    shapely>=1.3.0
+    # shapely 1.3+ required for Python 3 support
+    shapely>=1.3
+    # torch 1.7+ required for typing
     torch>=1.7
+    # torchvision 0.3+ required for download_file_from_google_drive
     torchvision>=0.3
 python_requires = >= 3.6
 packages = find:
@@ -49,30 +58,41 @@ datasets =
     h5py
     opencv-python
     pycocotools
+    # radiant-mlhub 0.2.1+ required for api_key bugfix:
+    # https://github.com/radiantearth/radiant-mlhub/pull/48
     radiant-mlhub>=0.2.1
+    # rarfile 3+ required for correct Rar file detection
     rarfile>=3
-    scipy>=0.9.0
-
-# Optional developer requirements
-docs =
-    ipywidgets>=7
-    jupyterlab
-    nbmake>=0.1
-    nbsphinx>=0.8.5
-    sphinx>=3
-    pydocstyle[toml]>=6.1
-    pytorch-sphinx-theme
-style =
-    black>=21.4b0
-    flake8>=3.8
-    isort[colors]>=5.8
-tests =
-    mypy>=0.900
-    pytest>=6
-    pytest-cov>=2.4
+    # scipy 0.9+ required for scipy.io.wavfile.read
+    scipy>=0.9
+# Optional trainer requirements
 train =
+    # omegaconf 2.1+ required for to_object method
     omegaconf>=2.1
+    # pytorch-lightning 1.3+ required for gradient_clip_algorithm argument to Trainer
     pytorch-lightning>=1.3
+    # scikit-learn 0.18+ required for sklearn.model_selection module
     scikit-learn>=0.18
+    # segmentation-models-pytorch 0.2+ required for smp.losses module
     segmentation-models-pytorch>=0.2
     torchmetrics
+# Optional developer requirements
+style =
+    # black 21+ required for Python 3.9 support
+    black>=21.4b0
+    # flake8 3.8+ depends on pyflakes 2.2+, which fixes a bug with mypy error code ignores:
+    # https://github.com/PyCQA/pyflakes/pull/455
+    flake8>=3.8
+    # isort 5.8+ required for extend_skip option
+    isort[colors]>=5.8
+    # pydocstyle 6.1+ required for pyproject.toml support
+    pydocstyle[toml]>=6.1
+tests =
+    # mypy 0.900+ required for pyproject.toml support
+    mypy>=0.900
+    # nbmake 0.1+ required to fix path_source bug
+    nbmake>=0.1
+    # pytest 6+ required for pyproject.toml support
+    pytest>=6
+    # pytest-cov 2.4+ required for pytest --cov flags
+    pytest-cov>=2.4

spack.yaml

@@ -1,40 +0,0 @@
-spack:
-  specs:
-  - "opencv+python3+imgcodecs+tiff+jpeg+png"
-  - "pil@2.9:"
-  - "python@3.6:+bz2"
-  - "py-black@21:"
-  - "py-einops"
-  - "py-fiona@1.5:"
-  - "py-flake8@3.8:"
-  - "py-h5py"
-  - "py-ipywidgets@7:"
-  - "py-isort@5.8:+colors"
-  - "py-jupyterlab"
-  - "py-matplotlib"
-  - "py-mypy@0.900:"
-  - "py-nbmake@0.1:"
-  - "py-nbsphinx@0.8.5:"
-  - "py-numpy"
-  - "py-omegaconf@2.1:"
-  - "py-pycocotools"
-  - "py-pydocstyle@6.1:+toml"
-  - "py-pyproj@2.2.0:"
-  - "py-pytest@6:"
-  - "py-pytest-cov@2.4:"
-  - "py-pytorch-lightning@1.3:"
-  - "py-pytorch-sphinx-theme"
-  - "py-radiant-mlhub@0.2.1:"
-  - "py-rarfile@3:"
-  - "py-rasterio@1.0.16:"
-  - "py-rtree@0.5:"
-  - "py-scikit-learn@0.18:"
-  - "py-scipy@0.9.0:"
-  - "py-segmentation-models-pytorch@0.2:"
-  - "py-setuptools@30.4:"
-  - "py-shapely@1.3.0:"
-  - "py-sphinx@3:"
-  - "py-torch@1.7:"
-  - "py-torchmetrics"
-  - "py-torchvision@0.3:"
-  concretization: together