Conda activate fix and development environment (#665)

* fixed bug in install_shapepipe * Added development environment. * added BigMac depdendency for macOS * activate dev environment * added cs_util to dev env * unpinned pip dependencies * updated install setup * set checkout action version * fix checkout action version * source Source Extractor from Conda-Forge * test Apple Silicon workflow * revert macOS runner * add gfortran to macOS deps * test reinstall of gcc to find gfortran * test without symlinks * update symlink script and dev requirements * update LDFLAGS and add license * test CXXFLAGS='-fcommon' for ww * test Ubuntu with gcc-9 * add Dockerfile and corresponding workflow * update CDS version * fix release CI trigger * removed Dockerfile and corresponding workflow * fix licence * use latest release of PySAP
CosmoStat · Oct 29, 2024 · 2b75551 · 2b75551
1 parent 1502cf8
commit 2b75551
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diff --git a/.github/workflows/ci-dev.yml b/.github/workflows/ci-dev.yml
@@ -0,0 +1,62 @@
+name: CI
+
+on:
+  pull_request:
+    branches:
+     - develop
+
+jobs:
+
+  test-full:
+    name: Full Test Suite
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: [3.11]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Linux dependencies
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get install libopenblas-dev gcc-9 g++-9
+
+      - name: Install macOS Dependencies
+        shell: bash -l {0}
+        if: runner.os == 'macOS'
+        run: |
+          brew tap sfarrens/sf
+          brew install bigmac libomp
+          brew reinstall gcc
+
+      - name: Set up conda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          auto-activate-base: true
+          miniforge-version: latest
+
+      - name: Install package (Linux)
+        shell: bash -l {0}
+        env:
+          CC: gcc-9
+          CXX: g++-9
+        if: runner.os == 'Linux'
+        run: ./install_shapepipe --env-dev
+
+      - name: Install package (macOS)
+        shell: bash -l {0}
+        if: runner.os == 'macOS'
+        run: ./install_shapepipe --env-dev
+
+      - name: Run tests
+        shell: bash -l {0}
+        run: |
+          conda activate shapepipe-dev
+          pytest
+          shapepipe_run -c example/config.ini
diff --git a/.github/workflows/ci-tests.yml → .github/workflows/ci-release.yml b/.github/workflows/ci-tests.yml → .github/workflows/ci-release.yml
@@ -5,48 +5,59 @@ on:
     branches:
      - main
      - master
-     - develop
 
 jobs:
 
   test-full:
     name: Full Test Suite
     runs-on: ${{ matrix.os }}
 
-    defaults:
-      run:
-        shell: bash -l {0}
-
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: [3.9]
+        python-version: [3.11]
 
     steps:
-      - name: Checkout
-        uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Install Linux dependencies
         if: runner.os == 'Linux'
-        run: sudo apt-get install libopenblas-dev
+        run: |
+          sudo apt-get install libopenblas-dev gcc-9 g++-9
 
       - name: Install macOS Dependencies
+        shell: bash -l {0}
         if: runner.os == 'macOS'
-        run: brew install libomp
+        run: |
+          brew tap sfarrens/sf
+          brew install bigmac libomp
+          brew reinstall gcc
 
       - name: Set up conda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
           auto-activate-base: true
+          miniforge-version: latest
+
+      - name: Install package (Linux)
+        shell: bash -l {0}
+        env:
+          CC: gcc-9
+          CXX: g++-9
+        if: runner.os == 'Linux'
+        run: ./install_shapepipe --develop
 
-      - name: Install package
+      - name: Install package (macOS)
+        shell: bash -l {0}
+        if: runner.os == 'macOS'
         run: ./install_shapepipe --develop
 
       - name: Run tests
+        shell: bash -l {0}
         run: |
-          conda activate shapepipe
-          python setup.py test
+          conda activate shapepipe-dev
+          pytest
           shapepipe_run -c example/config.ini
diff --git a/LICENSE b/LICENSE
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 CosmoStat
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/develop.txt b/develop.txt
diff --git a/docs/requirements.txt b/docs/requirements.txt
diff --git a/environment-dev.yml b/environment-dev.yml
@@ -0,0 +1,41 @@
+# ShapePipe Development Environment
+# ---------------------------------
+# This environment should only be used for development and testing of  
+# ShapePipe (i.e. nothing that could be published). Packages need only
+# specify the minimum compatible versions. This environment can updated 
+# as needed.
+name: shapepipe-dev
+channels:
+  - conda-forge
+dependencies:
+  - python=3.11
+  - pip>=21.2.4
+  - astropy>=5.0
+  - astromatic-source-extractor>=2.25.0
+  - autoconf>=2.71
+  - automake>=1.16
+  - cmake>=3.27
+  - galsim>=2.5
+  - joblib>=1.3
+  - libtool>=2.4
+  - matplotlib>=3.8
+  - numba>=0.57
+  - numpy>=1.22
+  - pandas>=2.1
+  - pyqt5-sip>=12.12
+  - pyqtgraph>=0.13
+  - reproject>=0.12
+  - sqlitedict>=2.1
+  - termcolor>=2.3
+  - tqdm>=4.66
+  - treecorr>=4.3
+  - wget
+  - pip:
+    - cs_util>=0.0.5
+    - mccd>=1.2.3
+    - modopt>=1.6
+    - sip_tpv>=1.1
+    - sf_tools>=2.0.4
+    - python-pysap>=0.2.1
+    - git+https://github.com/aguinot/ngmix@stable_version
+    - git+https://github.com/tobias-liaudat/Stile@v0.1