Merge branch 'master' into credibility-interval

handley-lab · May 15, 2024 · 3e6bd4b · 3e6bd4b
2 parents fe25aeb + 8726a90
commit 3e6bd4b
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diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml
@@ -12,8 +12,8 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
       - name: Upgrade pip and install linters
         run: |
           python -m pip install --upgrade pip
@@ -67,11 +67,14 @@ jobs:
             extras: true
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+      - name: Install hdf5 for macOS
+        if: ${{ matrix.os == 'macos-latest' }}
+        run: brew install hdf5 c-blosc
 
       - name: Install dependencies
         run: |
@@ -87,7 +90,10 @@ jobs:
         run: python -m pytest --cov=anesthetic tests
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+
 
   conda:
     runs-on: ${{ matrix.os }}
@@ -102,32 +108,37 @@ jobs:
             python-version: '3.11'
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           python-version: ${{ matrix.python-version }}
+      - name: Install hdf5 for macOS
+        if: ${{ matrix.os == 'macos-latest' }}
+        run: brew install hdf5 c-blosc
 
       - name: Install dependencies
         shell: bash -l {0}
         run: |
           conda config --append channels conda-forge
           conda install pytest pytest-cov
-          conda install scipy numpy 'matplotlib>=3.6.1' 'pandas>=2.0.0'
+          conda install scipy numpy 'matplotlib>=3.6.1,<3.9.0' 'pandas~=2.2.0'
 
       - name: Test with pytest
         shell: bash -l {0}
         run: python -m pytest --cov=anesthetic tests
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
 
   test-build-n-publish:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
       - name: Install pypa/build
@@ -145,21 +156,63 @@ jobs:
   minimum-dependencies:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python 3.9
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.9
 
-      - name: Install dependencies
+      - name: Upgrade pip and install tomli
         run: |
           python -m pip install --upgrade pip
           python -m pip install tomli
-          eval "python -m pip install $(./bin/min_dependencies.py)"
-          python -m pip install -e ".[test]"
+      - name: Install minimum dependencies
+        run: eval "python -m pip install $(./bin/min_dependencies.py)"
+      - name: Install anesthetic
+        run: python -m pip install -e ".[test]"
 
       - name: Test with pytest
-        run: python -m pytest --cov=anesthetic tests
+        run: python -m pytest tests
 
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v1
+  latest-dependencies:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up latest stable Python 3
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+
+      - name: Upgrade pip and install tomli
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install tomli
+      - name: Install latest dependencies
+        run: eval "python -m pip install $(./bin/latest_dependencies.py)"
+      - name: Install pytest and anesthetic
+        run: |
+          python -m pip install pytest
+          python -m pip install --no-deps -e .
+
+      - name: Test with pytest
+        run: python -m pytest tests
+
+  check-for-new-versions:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up latest stable Python 3
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+
+      - name: Upgrade pip and install tomli and requests
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install tomli requests
+
+      - name: Install anesthetic
+        run: python -m pip install -e ".[test]"
+
+      - name: Check anesthetic dependencies are up to date
+        run: python -m pytest ./bin/check_up_to_date.py
diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
@@ -4,14 +4,23 @@ on:
     branches:
       - master
 jobs:
-  git-tag-and-release:
+  get-version:
     runs-on: ubuntu-latest
+    outputs:
+      version: ${{ steps.step1.outputs.v }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Get version number
-        run: |
-          VERSION="$(grep ':Version:' README.rst | awk '{print $2}')"
-          echo "DIST_VERSION=v${VERSION}" >> $GITHUB_ENV
+        id: step1 
+        run: echo "v=$(grep ':Version:' README.rst | awk '{print $2}')" >> $GITHUB_OUTPUT
+
+  git-tag-and-release:
+    runs-on: ubuntu-latest
+    needs: get-version
+    steps:
+      - uses: actions/checkout@v4
+      - name: set version number
+        run: echo "DIST_VERSION=v${{ needs.get-version.outputs.version }}" >> $GITHUB_ENV
       - name: Create Tag
         uses: actions/github-script@v6
         with:
@@ -34,9 +43,9 @@ jobs:
   pypi-release:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
       - name: Install pypa/build
@@ -48,13 +57,27 @@ jobs:
         with:
           password: ${{ secrets.PYPI_API_TOKEN }}
 
+  pypi-public:
+    needs: 
+      - get-version
+      - pypi-release
+    runs-on: ubuntu-latest
+    steps:
+      - name: Wait for PyPi
+        uses: nev7n/wait_for_response@v1
+        with:
+          url: "https://files.pythonhosted.org/packages/source/a/anesthetic/anesthetic-${{ needs.get-version.outputs.version }}.tar.gz"
+          responseCode: 200
+          timeout: 600000
+          interval: 10000
+
   aur-release:
-    needs: pypi-release
+    needs: pypi-public
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
       - name: Install dependencies
@@ -63,17 +86,6 @@ jobs:
           python -m pip install tomli
       - name: Generate PKGBUILD
         run: python ./bin/gen_PKGBUILD.py > ./PKGBUILD
-      - name: Get version number
-        run: |
-          VERSION="$(cat ./PKGBUILD | grep pkgver= | awk -F= '{print $2}')"
-          echo "DIST_VERSION=${VERSION}" >> $GITHUB_ENV
-      - name: Wait for PyPi
-        uses: nev7n/wait_for_response@v1
-        with:
-          url: "https://files.pythonhosted.org/packages/source/a/anesthetic/anesthetic-${{ env.DIST_VERSION }}.tar.gz"
-          responseCode: 200
-          timeout: 600000
-          interval: 10000
       - name: Publish AUR package
         uses: KSXGitHub/[email protected]
         with:
@@ -83,3 +95,74 @@ jobs:
           commit_username: ${{ secrets.AUR_USERNAME }}
           commit_email: ${{ secrets.AUR_EMAIL }}
           ssh_private_key: ${{ secrets.AUR_SSH_PRIVATE_KEY }}
+
+  conda-release:
+    needs: pypi-public
+    name: Build and deploy to conda
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Conda environment creation and activation
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: 3.11
+          auto-update-conda: false
+          auto-activate-base: false
+          show-channel-urls: true
+      - name: install dependencies
+        shell: bash -el {0}
+        run: conda install grayskull conda-build anaconda-client
+      - name: Generate meta.yaml from grayskull
+        shell: bash -el {0}
+        run: grayskull pypi --strict-conda-forge anesthetic
+      - name: Build and upload the conda packages
+        uses: uibcdf/[email protected]
+        with:
+          meta_yaml_dir: anesthetic
+          python-version: 3.11
+          user: handley-lab
+          label: 'main'
+          token: ${{ secrets.ANACONDA_TOKEN }} # Replace with the right name of your secret
+
+  conda-build:
+    needs: 
+      - conda-release
+      - get-version
+    name: test installation from conda
+    runs-on: ubuntu-latest
+    steps:
+      - name: Conda environment creation and activation
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: 3.11
+          auto-update-conda: false
+          auto-activate-base: false
+          show-channel-urls: true
+      - name: install from conda
+        shell: bash -el {0}
+        run: conda install -c handley-lab anesthetic
+      - name: get install version
+        shell: bash -el {0}
+        run: echo "install_version=$(python -c 'import anesthetic; print(anesthetic.__version__)')" >> $GITHUB_ENV
+      - name: fail if versions not matching
+        if: ${{ env.install_version != needs.get-version.outputs.version }}
+        run: exit 1
+
+  pypi-build:
+    needs: 
+      - pypi-public
+      - get-version
+    name: test installation from pypi
+    runs-on: ubuntu-latest
+    steps:
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+      - name: Install from pypi
+        run: pip install anesthetic
+      - name: get install version
+        run: echo "install_version=$(python -c 'import anesthetic; print(anesthetic.__version__)')" >> $GITHUB_ENV
+      - name: fail if versions not matching
+        if: ${{ env.install_version != needs.get-version.outputs.version }}
+        run: exit 1
diff --git a/.github/workflows/version.yaml b/.github/workflows/version.yaml
@@ -8,8 +8,8 @@ jobs:
   version-is-unit-incremented:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
       - name: Upgrade pip and install linters
         run: |
           python -m pip install --upgrade pip

diff --git a/.gitignore b/.gitignore
@@ -13,3 +13,5 @@ plikHM_TTTEEE_lowl_lowE_lensing_NS/
 *~
 .pytest_cache/*
 .coverage
+
+.DS_Store
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -9,7 +9,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.8"
+    python: "3.11"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

diff --git a/README.rst b/README.rst
@@ -2,7 +2,7 @@
 anesthetic: nested sampling post-processing
 ===========================================
 :Authors: Will Handley and Lukas Hergt
-:Version: 2.5.0
+:Version: 2.9.0
 :Homepage: https://github.com/handley-lab/anesthetic
 :Documentation: http://anesthetic.readthedocs.io/
 
@@ -18,6 +18,9 @@ anesthetic: nested sampling post-processing
 .. image:: https://badge.fury.io/py/anesthetic.svg
    :target: https://badge.fury.io/py/anesthetic
    :alt: PyPi location
+.. image:: https://anaconda.org/handley-lab/anesthetic/badges/version.svg
+   :target: https://anaconda.org/handley-lab/anesthetic
+   :alt: Conda location
 .. image:: https://zenodo.org/badge/175663535.svg
    :target: https://zenodo.org/badge/latestdoi/175663535
    :alt: Permanent DOI for this release
@@ -72,7 +75,13 @@ Installation
 
     pip install anesthetic
 
-or from the repository
+via conda
+
+.. code:: bash
+
+    conda install -c handley-lab anesthetic
+
+or from the github repository
 
 .. code:: bash
 
@@ -96,7 +105,7 @@ Dependencies
 
 Basic requirements:
 
-- Python 3.6+
+- Python 3.9+
 - `matplotlib <https://pypi.org/project/matplotlib/>`__
 - `numpy <https://pypi.org/project/numpy/>`__
 - `scipy <https://pypi.org/project/scipy/>`__