Support builds on windows, linux, and osx (#3)

* Fix build on windows * Switch to conda build * Remove cuda dependencies * Set default actions shell to bash * Fix conda install on windows in GH actions test * Set bash as default shell * Test python 3.8 and 3.9 * Downgrade numpy See brycefrank/pyfor#78 * Tidy up action workflow * Fix install
HakaiInstitute · Feb 24, 2022 · 773b4d8 · 773b4d8
1 parent eb00fe5
commit 773b4d8
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Showing 16 changed files with 95 additions and 50 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -1,5 +1,5 @@
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+# For more information see: https:/help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
 name: Tests
 
@@ -10,32 +10,34 @@ on:
     branches: [ main ]
 
 jobs:
-  build:
+  test:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.8", "3.9"]
+        os: [ ubuntu-latest, macos-latest, windows-latest ]
+        python-version: [ "3.8", "3.9" ]
     runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Setup Poetry
-      uses: abatilo/[email protected]
-      with:
-        poetry-version: 1.1
-    - name: Install dependencies
-      run: |
-        poetry install
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        poetry run flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        poetry run flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
-      run: |
-        poetry run pytest
+      - name: Checkout code
+        uses: actions/checkout@v2
+      - name: Install dependencies
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          environment-file: environment.yml
+          python-version: ${{ matrix.python-version }}
+          auto-update-conda: true
+          auto-activate-base: true
+      - name: Lint with flake8
+        run: |
+          conda install flake8
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Test with pytest
+        run: |
+          conda install pytest
+          pytest
diff --git a/.idea/hakai-segmentation.iml b/.idea/hakai-segmentation.iml
diff --git a/conda/hakai_segmentation/meta.yaml b/conda/hakai_segmentation/meta.yaml
@@ -0,0 +1,50 @@
+{% set name = "hakai_segmentation" %}
+{% set version = "0.1.0rc2" %}
+
+package:
+  name: "{{ name|lower }}"
+  version: "{{ version }}"
+
+source:
+  path: ../../
+
+build:
+  noarch: python
+  number: 0
+  entry_points:
+    - kom = hakai_segmentation.cli:cli
+  script: "{{ PYTHON }} -m pip install . -vv"
+
+requirements:
+  host:
+    - python
+    - pip
+    - poetry
+  run:
+    - python
+    - fire >=0.4.0,<0.5.0
+    - numpy >=1.22.2,<2.0.0
+    - rasterio >=1.2.10,<2.0.0
+    - pytorch >=1.10.2,<2.0.0
+    - torchvision >=0.11.3,<0.12.0
+    - tqdm >=4.62.3,<5.0
+
+test:
+  imports:
+    - hakai_segmentation
+    - hakai_segmentation.data
+    - hakai_segmentation.geotiff_io
+  commands:
+    - kom --help
+
+about:
+  home: "https://github.com/hakaiInstitute/hakai-segmentation"
+  license: MIT
+  license_file: LICENSE.txt
+  summary: "Hakai Segment Tool for GeoTiff RPAS Imagery"
+  doc_url: "https://hakai-segmentation.readthedocs.io"
+  dev_url: "https://github.com/hakaiInstitute/hakai-segmentation"
+
+extra:
+  recipe-maintainers:
+    - tayden
diff --git a/environment.yml b/environment.yml
@@ -0,0 +1,13 @@
+name: hakai-segmentation
+channels:
+  - pytorch
+  - conda-forge
+  - defaults
+dependencies:
+  - python>=3.8,<3.10
+  - conda-forge::fire
+  - conda-forge::numpy
+  - conda-forge::rasterio
+  - conda-forge::tqdm
+  - pytorch::pytorch>=1.10
+  - pytorch::torchvision
diff --git a/hakai_segmentation/cli.py b/hakai_segmentation/cli.py
@@ -1,6 +1,6 @@
 import fire
 
-from hakai_segmentation import find_kelp, find_mussels
+from hakai_segmentation.lib import find_kelp, find_mussels
 
 
 def cli():

diff --git a/hakai_segmentation/geotiff_io/__init__.py b/hakai_segmentation/geotiff_io/__init__.py
@@ -1,4 +1,4 @@
 from hakai_segmentation.geotiff_io.geotiff_reader import GeotiffReader
 from hakai_segmentation.geotiff_io.geotiff_writer import GeotiffWriter
 
-__all__ = [GeotiffReader, GeotiffWriter]
+__all__ = ['GeotiffReader', 'GeotiffWriter']
diff --git a/hooks/hook-rasterio.py b/hooks/hook-rasterio.py
diff --git a/pyproject.toml b/pyproject.toml
@@ -6,6 +6,7 @@ authors = ["Taylor Denouden <[email protected]>"]
 license = "MIT"
 readme = "README.rst"
 repository = "https://github.com/hakaiInstitute/hakai-segmentation"
+documentation = "https://hakai-segmentation.readthedocs.io"
 
 packages = [
     { include = "hakai_segmentation" }
@@ -21,19 +22,7 @@ tqdm = "^4.62.3"
 torchvision = "^0.11.3"
 torch = "^1.10.2"
 fire = "^0.4.0"
-rasterio = [
-    { version = "^1.2.10", platform = "linux || darwin" },
-    { path = "windows/rasterio-1.2.10-cp38-cp38-win32.whl", markers = "python_version == '3.8' and platform_system == 'Windows' and platform_machine == 'x86_64'" },
-    { path = "windows/rasterio-1.2.10-cp39-cp39-win32.whl", markers = "python_version == '3.9' and platform_system == 'Windows' and platform_machine == 'x86_64'" },
-    { path = "windows/rasterio-1.2.10-cp38-cp38-win_amd64.whl", markers = "python_version == '3.8' and platform_system == 'Windows' and platform_machine == 'AMD64'" },
-    { path = "windows/rasterio-1.2.10-cp39-cp39-win_amd64.whl", markers = "python_version == '3.9' and platform_system == 'Windows' and platform_machine == 'AMD64'" },
-]
-gdal = [
-    { path = "windows/GDAL-3.4.1-cp38-cp38-win32.whl", markers = "python_version == '3.8' and platform_system == 'Windows' and platform_machine == 'x86_64'" },
-    { path = "windows/GDAL-3.4.1-cp39-cp39-win32.whl", markers = "python_version == '3.9' and platform_system == 'Windows' and platform_machine == 'x86_64'" },
-    { path = "windows/GDAL-3.4.1-cp38-cp38-win_amd64.whl", markers = "python_version == '3.8' and platform_system == 'Windows' and platform_machine == 'AMD64'" },
-    { path = "windows/GDAL-3.4.1-cp39-cp39-win_amd64.whl", markers = "python_version == '3.9' and platform_system == 'Windows' and platform_machine == 'AMD64'" },
-]
+rasterio = "^1.2.1"
 
 [tool.poetry.dev-dependencies]
 pytest = "^7.0.1"

diff --git a/windows/GDAL-3.4.1-cp38-cp38-win32.whl b/windows/GDAL-3.4.1-cp38-cp38-win32.whl
diff --git a/windows/GDAL-3.4.1-cp38-cp38-win_amd64.whl b/windows/GDAL-3.4.1-cp38-cp38-win_amd64.whl
diff --git a/windows/GDAL-3.4.1-cp39-cp39-win32.whl b/windows/GDAL-3.4.1-cp39-cp39-win32.whl
diff --git a/windows/GDAL-3.4.1-cp39-cp39-win_amd64.whl b/windows/GDAL-3.4.1-cp39-cp39-win_amd64.whl
diff --git a/windows/rasterio-1.2.10-cp38-cp38-win32.whl b/windows/rasterio-1.2.10-cp38-cp38-win32.whl
diff --git a/windows/rasterio-1.2.10-cp38-cp38-win_amd64.whl b/windows/rasterio-1.2.10-cp38-cp38-win_amd64.whl
diff --git a/windows/rasterio-1.2.10-cp39-cp39-win32.whl b/windows/rasterio-1.2.10-cp39-cp39-win32.whl
diff --git a/windows/rasterio-1.2.10-cp39-cp39-win_amd64.whl b/windows/rasterio-1.2.10-cp39-cp39-win_amd64.whl