Sparse2D version 3 (#183)

* deprecated pyqtgraph usage * build CFITSIO from source * added bigmac dependency for macOS * test update to conda activation * update ci matrix * clean up code style * switched to testing framework to pytest * removed Python 3.6 test case * check C compilers * check pysparse installation * added checking step to CI * test with LD_LIBRARY_PATH * Update pysap/plotting/transform.py Co-authored-by: Pierre-Antoine Comby <[email protected]> * Update pysap/configure.py Co-authored-by: Pierre-Antoine Comby <[email protected]> * add changes suggested by reviewer Co-authored-by: Pierre-Antoine Comby <[email protected]>
CEA-COSMIC · Jan 19, 2023 · f5abaf3 · f5abaf3
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commit f5abaf3
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Showing 28 changed files with 218 additions and 2,765 deletions.
diff --git a/.github/workflows/cd-build.yml b/.github/workflows/cd-build.yml
@@ -16,24 +16,24 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v2
 
-      - name: Set up Conda with Python 3.9
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
         with:
-          auto-update-conda: true
-          python-version: 3.9
-          auto-activate-base: false
+          python-version: ${{ matrix.python-version }}
+
+      - name: Check Python Version
+        run: python --version
 
       - name: Install Package Dependencies
-        shell: bash -l {0}
         run: |
-          python --version
           python -m pip install --upgrade pip
-          python -m pip install nose nose-exclude coverage pycodestyle
+          python -m pip install -r develop.txt
+
+      - name: Install PySAP
+        run: python -m pip install .
 
       - name: Run Tests
-        shell: bash -l {0}
-        run: |
-          python setup.py nosetests
+        run: python -m pytest
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v1
@@ -57,23 +57,22 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v2
 
-      - name: Set up Conda with Python 3.9
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
         with:
-          auto-update-conda: true
-          python-version: 3.9
-          auto-activate-base: false
+          python-version: ${{ matrix.python-version }}
+
+      - name: Check Python Version
+        run: python --version
 
       - name: Install dependencies
-        shell: bash -l {0}
         run: |
-          conda install -c conda-forge pandoc
           python -m pip install --upgrade pip
+          python -m pip install pandoc
           python -m pip install -r docs/requirements.txt
           python -m pip install .
 
       - name: Download plug-ins
-        shell: bash -l {0}
         if: ${{ inputs.build_plugins }}
         run: |
           while read _plugin; do
@@ -85,7 +84,6 @@ jobs:
           rm *.tar.gz
 
       - name: Extract plug-in examples
-        shell: bash -l {0}
         if: ${{ inputs.build_examples }}
         run: |
           while read _plugin; do
@@ -95,11 +93,9 @@ jobs:
           done < plugins.txt
 
       - name: Build PySAP source files
-        shell: bash -l {0}
         run: sphinx-apidoc ${sphinx_opts} pysap
 
       - name: Build plug-in source files
-        shell: bash -l {0}
         if: ${{ inputs.build_plugins }}
         run: |
           while read _plugin; do
@@ -109,7 +105,6 @@ jobs:
           done < plugins.txt
 
       - name: Build API documentation
-        shell: bash -l {0}
         run: sphinx-build -E docs/source docs/_build
 
       - name: Deploy API documentation

diff --git a/.github/workflows/check-docs.yml b/.github/workflows/check-docs.yml
@@ -29,23 +29,22 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v2
 
-      - name: Set up Conda with Python 3.9
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
         with:
-          auto-update-conda: true
-          python-version: 3.9
-          auto-activate-base: false
+          python-version: ${{ matrix.python-version }}
+
+      - name: Check Python Version
+        run: python --version
 
       - name: Install dependencies
-        shell: bash -l {0}
         run: |
-          conda install -c conda-forge pandoc
           python -m pip install --upgrade pip
+          python -m pip install pandoc
           python -m pip install -r docs/requirements.txt
           python -m pip install .
 
       - name: Download plug-ins
-        shell: bash -l {0}
         if: ${{ inputs.build_plugins }}
         run: |
           while read _plugin; do
@@ -57,7 +56,6 @@ jobs:
           rm *.tar.gz
 
       - name: Extract plug-in examples
-        shell: bash -l {0}
         if: ${{ inputs.build_examples }}
         run: |
           while read _plugin; do
@@ -67,11 +65,9 @@ jobs:
           done < plugins.txt
 
       - name: Build PySAP source files
-        shell: bash -l {0}
         run: sphinx-apidoc ${sphinx_opts} pysap
 
       - name: Build plug-in source files
-        shell: bash -l {0}
         if: ${{ inputs.build_plugins }}
         run: |
           while read _plugin; do
@@ -81,13 +77,11 @@ jobs:
           done < plugins.txt
 
       - name: Build API documentation
-        shell: bash -l {0}
         run: sphinx-build -E docs/source docs/_build
 
       - name: Archive API build
         uses: actions/upload-artifact@v2
         with:
           name: api-docs
           retention-days: 14
-          path: |
-            docs/_build
+          path: docs/_build
diff --git a/.github/workflows/ci-build.yml b/.github/workflows/ci-build.yml
@@ -16,63 +16,55 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: [3.8]
+        python-version: ["3.10"]
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
-      - name: Set up Conda with Python ${{ matrix.python-version }}
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
         with:
-          auto-update-conda: true
           python-version: ${{ matrix.python-version }}
-          auto-activate-base: false
 
-      - name: Check Conda
-        shell: bash -l {0}
-        run: |
-          conda info
-          conda list
-          python --version
+      - name: Check Python Version
+        run: python --version
 
       - name: Install macOS Dependencies
-        shell: bash -l {0}
         if: runner.os == 'macOS'
         run: |
-          brew install libomp
+          brew tap sfarrens/sf
+          brew install bigmac libomp
 
       - name: Install Package Dependencies
-        shell: bash -l {0}
         run: |
-          python --version
           python -m pip install --upgrade pip
-          python -m pip install nose nose-exclude coverage pycodestyle
+          python -m pip install -r develop.txt
           python -m pip install twine
 
-      - name: Run Tests
-        shell: bash -l {0}
+      - name: Install PySAP
+        run: python -m pip install .
+
+      - name: Check PySAP Installation
         run: |
-          python setup.py nosetests
-          pycodestyle pysap --ignore="E121,E123,E126,E226,E24,E704,E402,E731,E722,E741,W503,W504,W605"
-          pycodestyle examples --ignore="E121,E123,E126,E226,E24,E704,E402,E731,E741,W503,W504,W605"
+          python -c "import pysparse"
+          python -c "import pysap; print(pysap.info())"
+
+      - name: Run Tests
+        run: python -m pytest
 
       - name: Save Test Results
         if: always()
         uses: actions/upload-artifact@v2
         with:
           name: unit-test-results-${{ matrix.os }}-${{ matrix.python-version }}
-          path: nosetests.xml
+          path: pytest.xml
 
       - name: Run Examples
         continue-on-error: true
-        shell: bash -l {0}
-        run: |
-          python -m pip install .
-          python pysap/test/test_examples.py
+        run: python pysap/test/test_examples.py
 
       - name: Check Distribution
-        shell: bash -l {0}
         run: |
           python setup.py sdist
           twine check dist/*
@@ -92,33 +84,39 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: [3.6, 3.7, 3.9]
+        python-version: ["3.7", "3.8", "3.9"]
 
     steps:
       - name: Checkout
         uses: actions/checkout@v2
 
-      - name: Set up Conda with Python ${{ matrix.python-version }}
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
         with:
-          auto-update-conda: true
           python-version: ${{ matrix.python-version }}
-          auto-activate-base: false
+
+      - name: Check Python Version
+        run: python --version
 
       - name: Install macOS Dependencies
-        shell: bash -l {0}
         if: runner.os == 'macOS'
         run: |
-          brew install libomp
+          brew tap sfarrens/sf
+          brew install bigmac libomp
 
       - name: Install Package Dependencies
-        shell: bash -l {0}
         run: |
           python --version
           python -m pip install --upgrade pip
-          python -m pip install nose nose-exclude coverage pycodestyle
+          python -m pip install -r develop.txt
 
-      - name: Run Tests
-        shell: bash -l {0}
+      - name: Install PySAP
+        run: python -m pip install .
+
+      - name: Check PySAP Installation
         run: |
-          python setup.py nosetests
+          python -c "import pysparse"
+          python -c "import pysap; print(pysap.info())"
+
+      - name: Run Tests
+        run: python -m pytest
diff --git a/develop.txt b/develop.txt
@@ -0,0 +1,3 @@
+pytest
+pytest-cov
+pytest-pycodestyle
diff --git a/environment.yml b/environment.yml
@@ -3,8 +3,9 @@ channels:
   - conda-forge
   - astra-toolbox
 dependencies:
-  - python=3.9
+  - python=3.10
   - astra-toolbox>=2.0.0
+  - cmake>=3.12.0
   - jupyter>=1.0.0
   - matplotlib>=3.3.4
   - pynfft>=1.3.2
@@ -17,7 +18,6 @@ dependencies:
     - nibabel>=3.2.1
     - numpy>=1.19.5
     - progressbar2>=3.53.1
-    - pyqtgraph>=0.11.1
     - PyWavelets>=1.1.1
     - scikit-image>=0.17.2
     - scikit-learn>=0.24.1

diff --git a/pysap/base/image.py b/pysap/base/image.py
@@ -9,6 +9,7 @@
 
 # System import
 import numpy
+from warnings import warn
 
 # Package import
 from .observable import Observable
@@ -88,6 +89,12 @@ def __init__(self, shape=None, spacing=None, data_type="scalar",
     def show(self):
         """ Display the image data.
         """
+        warn(
+            'The show method has been deprecated and will be removed in a '
+            + 'future release. In the future Please use the Image.data '
+            + 'attribute and your plotting package of choice.',
+            FutureWarning
+        )
         plot_data(self.data, scroll_axis=self._scroll_axis)
 
     def modified(self):

diff --git a/pysap/base/plugins.py b/pysap/base/plugins.py
@@ -33,7 +33,7 @@ def find_module(self, name, path=None):
         package/module-finding code kicks in.
         """
         # Use this loader only on registered modules
-        match = re.match("pysap\.plugins\.(.*)", name)
+        match = re.match(r"pysap\.plugins\.(.*)", name)
         if match is None:
             return None
         name = match.groups()[0]

diff --git a/pysap/base/transform.py b/pysap/base/transform.py
@@ -15,7 +15,7 @@
 from pprint import pprint
 import uuid
 import os
-import warnings
+from warnings import warn
 
 # Package import
 import pysap
@@ -352,6 +352,14 @@ def bands_shapes(cls, bands_lengths, ratio=None):
     def show(self):
         """ Display the different bands at the different decomposition scales.
         """
+        warn(
+            'The show method has been deprecated and will be removed in a '
+            + 'future release. In the future Please use the Transform.data '
+            + 'and/or Transform.analysis_data attributes and your plotting '
+            + 'package of choice. To use this deprecated function you will '
+            + 'need to install pyqtgraph manually.',
+            FutureWarning
+        )
         plot_transform(self)
 
     def analysis(self, **kwargs):

diff --git a/pysap/configure.py b/pysap/configure.py
@@ -50,7 +50,7 @@ def _check_python_versions():
             mod_name = "pywt"
         try:
             mod_install_version = importlib.import_module(mod_name).__version__
-        except:
+        except ImportError:
             mod_install_version = "?"
         versions[mod_name] = (operator + mod_min_version, mod_install_version)
     return versions