Merge pull request #557 from eqcorrscan/develop

Merge for new release
eqcorrscan · Dec 11, 2023 · acf20c3 · acf20c3
2 parents 886aa38 + 137690c
commit acf20c3
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Showing 71 changed files with 6,727 additions and 3,459 deletions.
diff --git a/.coveragerc b/.coveragerc
@@ -1,6 +1,7 @@
 [run]
 branch = True
 source = eqcorrscan
+concurrency = multiprocessing,thread
 omit =
   eqcorrscan/__init__.py
   eqcorrscan/*/__init__.py

diff --git a/.github/test_conda_env.yml b/.github/test_conda_env.yml
@@ -5,9 +5,9 @@ channels:
 dependencies:
   - numpy>=1.12
   - matplotlib>=1.3.0
-  - scipy>=0.18,<1.9.0  # Pinned due to scipy/obspy hanning renaming
+  - scipy
   - mock
-  - obspy>=1.3.0
+  - obspy>=1.4.0
   - h5py
   - pyyaml
   - bottleneck
@@ -17,8 +17,6 @@ dependencies:
   - pytest-pep8
   - pytest-xdist
   - pytest-rerunfailures
-  - pytest-mpl<0.16.0
+  - pytest-mpl
   - codecov
-  - pip
-  - pip:
-    - pyfftw
+  - boto3
diff --git a/.github/test_conda_env_macOS.yml b/.github/test_conda_env_macOS.yml
@@ -1,23 +1,28 @@
 name: eqcorrscan-test
 channels:
   - conda-forge
-  - defaults
 dependencies:
-  - clangdev>=4
-  - openmp>=4
-  - libcxx>=4
-  - cctools
-  - clang
+  # Compiler bits to match conda-forge build env
+  - cctools_osx-64
+  - clang=14
+  - clang-14
   - clang_osx-64
+  - llvm-openmp
+  - clangxx=14
   - compiler-rt
-  - libcxx
-  - llvm-openmp>=4.0.1
+  - compiler-rt_osx-64
+  - ld64_osx-64
+  - libclang-cpp14
+  - libcxx=14
+  - libllvm14
+  - llvm-tools  
+  # Normal requirements
   - numpy>=1.12
   - matplotlib>=1.3.0
-  - scipy>=0.18,<1.9.0  # Pinned due to scipy/obspy hanning renaming
+  - scipy
   - mock
-  - obspy>=1.3.0
-  - h5py<3.2  # Issue with dep resolution: https://github.com/conda-forge/h5py-feedstock/issues/92
+  - obspy>=1.4.0
+  - h5py>3.3  # Issue with dep resolution: https://github.com/conda-forge/h5py-feedstock/issues/92
   - pyyaml
   - bottleneck
   - fftw
@@ -28,6 +33,4 @@ dependencies:
   - pytest-rerunfailures
   - pytest-mpl<0.16.0
   - codecov
-  - pip
-  - pip:
-    - pyfftw
+  - boto3
diff --git a/.github/workflows/flake8-linter-matcher.json b/.github/workflows/flake8-linter-matcher.json
@@ -0,0 +1,17 @@
+{
+    "problemMatcher": [
+        {
+            "owner": "flake8-linter-error",
+            "severity": "error",
+            "pattern": [
+                {
+                    "regexp": "^([^:]+):(\\d+):(\\d+):\\s+([EWCNF]\\d+\\s+.+)$",
+                    "file": 1,
+                    "line": 2,
+                    "column": 3,
+                    "message": 4
+                }
+            ]
+        }
+    ]
+}
diff --git a/.github/workflows/flake8.yml b/.github/workflows/flake8.yml
@@ -0,0 +1,27 @@
+name: Flake8 Linter
+on:
+  pull_request:
+jobs:
+  flake8-linter:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v3
+      - name: Install Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+      - name: Install Flake8 5.0.4 linter
+        run: pip install flake8==5.0.4  # use this version for --diff option
+      - name: Setup Flake8 output matcher for PR annotations
+        run: echo '::add-matcher::.github/workflows/flake8-linter-matcher.json'
+      - name: Fetch pull request target branch
+        run: |
+          git remote add upstream https://github.com/eqcorrscan/EQcorrscan.git
+          git fetch upstream $GITHUB_BASE_REF
+      - name: Run Flake8 linter
+        run: git diff upstream/$GITHUB_BASE_REF HEAD | flake8
+          --exclude eqcorrscan/doc
+          --ignore W605,W504,W503
+          --max-line-length 80
+          --diff
diff --git a/.github/workflows/runtest.yml b/.github/workflows/runtest.yml
@@ -8,12 +8,12 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.7', '3.8', '3.9']
+        python-version: ['3.8', '3.9', '3.10', '3.11']
       fail-fast: false
 #      continue-on-error: true
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Get conda env file
         shell: bash -l {0}
@@ -22,31 +22,22 @@ jobs:
               cp .github/test_conda_env_macOS.yml .github/test_conda_env.yml
           fi
 
-      - name: Cache conda
-        uses: actions/cache@v2
-        env:
-          # Increase this value to reset cache if needed by env file has not changed
-          CACHE_NUMBER: 0
-        with:
-          path: ~/conda_pkgs_dir
-          key:
-            ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
-            hashFiles('.github/test_conda_env.yml') }}
-
       - name: Setup conda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v2.1.1
         with:
-          miniconda-version: 'latest'
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
           python-version: ${{ matrix.python-version }}
           activate-environment: eqcorrscan-test
-          environment-file: .github/test_conda_env.yml
-          condarc-file: .github/test_condarc.yml
-          use-only-tar-bz2: true  # Must be set for caching to work properly
+          use-mamba: true
+
+      - name: Update Env
+        run: mamba env update -n eqcorrscan-test -f .github/test_conda_env.yml
 
       - name: install eqcorrscan
         shell: bash -l {0}
         run: |
-          pip install -e .
+          pip install -v -e . --no-deps
 
       - name: print package info
         shell: bash -l {0}
@@ -65,7 +56,7 @@ jobs:
       - name: run main test suite
         shell: bash -l {0}
         run: |
-          py.test -n 2 -m "not serial and not network and not superslow" --cov-report=xml --dist loadscope
+          py.test -n 2 -m "not serial and not network and not superslow and not slow" --cov-report=xml --dist loadscope
 
       - name: run serial test
         if: always()
@@ -81,7 +72,7 @@ jobs:
           py.test -v -m "slow and not serial and not network" --cov-report=xml --cov-append
 
       - name: upload coverage
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v3
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml
@@ -95,37 +86,28 @@ jobs:
     runs-on: "ubuntu-latest"
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: ['3.10']
       fail-fast: false
 
     steps:
-      - uses: actions/checkout@v2
-
-      - name: Cache conda
-        uses: actions/cache@v2
-        env:
-          # Increase this value to reset cache if needed by env file has not changed
-          CACHE_NUMBER: 0
-        with:
-          path: ~/conda_pkgs_dir
-          key:
-            ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
-            hashFiles('.github/test_conda_env.yml') }}
+      - uses: actions/checkout@v3
 
       - name: Setup conda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v2.1.1
         with:
-          miniconda-version: 'latest'
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
           python-version: ${{ matrix.python-version }}
           activate-environment: eqcorrscan-test
-          environment-file: .github/test_conda_env.yml
-          condarc-file: .github/test_condarc.yml
-          use-only-tar-bz2: true  # Must be set for caching to work properly
+          use-mamba: true
+
+      - name: Update Env
+        run: mamba env update -n eqcorrscan-test -f .github/test_conda_env.yml
 
       - name: install eqcorrscan
         shell: bash -l {0}
         run: |
-          pip install -e .
+          pip install -e . --no-deps
 
       - name: print package info
         shell: bash -l {0}
@@ -136,7 +118,7 @@ jobs:
       - name: run network tests
         shell: bash -l {0}
         run: |
-          py.test -n 2 -m "network" --cov-report=xml
+          py.test -n 2 -m "network and not superslow" --cov-report=xml
       - name: run tutorials
         if: always()
         shell: bash -l {0}
@@ -149,7 +131,7 @@ jobs:
           py.test -m "superslow" -s eqcorrscan/tests/tutorials_test.py eqcorrscan/tests/subspace_test.py --cov-report=xml --cov-append
 
       - name: upload coverage
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v3
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml
@@ -162,40 +144,31 @@ jobs:
     runs-on: "ubuntu-latest"
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: ['3.9']
       fail-fast: false
 
     steps:
-      - uses: actions/checkout@v2
-
-      - name: Cache conda
-        uses: actions/cache@v2
-        env:
-          # Increase this value to reset cache if needed by env file has not changed
-          CACHE_NUMBER: 0
-        with:
-          path: ~/conda_pkgs_dir
-          key:
-            ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
-            hashFiles('.github/test_conda_env.yml') }}
-
+      - uses: actions/checkout@v3
+
       - name: Setup conda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v2.1.1
         with:
-          miniconda-version: 'latest'
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
           python-version: ${{ matrix.python-version }}
           activate-environment: eqcorrscan-test
-          environment-file: .github/test_conda_env.yml
-          condarc-file: .github/test_condarc.yml
-          use-only-tar-bz2: true  # Must be set for caching to work properly
+          use-mamba: true
+
+      - name: Update Env
+        run: mamba env update -n eqcorrscan-test -f .github/test_conda_env.yml
 
       - name: install fmf
         shell: bash -l {0}
         run: |
           cd ..
           git clone https://github.com/beridel/fast_matched_filter.git
           cd fast_matched_filter
-          pip install -e .
+          pip install -e . --no-deps
           cd ../EQcorrscan
 
       - name: install eqcorrscan
@@ -216,7 +189,7 @@ jobs:
           py.test eqcorrscan/tests/correlate_test.py --cov-report=xml
 
       - name: upload coverage
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v3
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -16,7 +16,8 @@ sphinx:
   configuration: eqcorrscan/doc/conf.py
 
 # Optionally build your docs in additional formats such as PDF and ePub
-formats: all
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html#formats
+formats: []
 
 # Optionally set the version of Python and requirements required to build your docs
 python:

diff --git a/.stickler.yml b/.stickler.yml