From cb028641c4c50405dffbd763da88f07e9433d668 Mon Sep 17 00:00:00 2001
From: Antony Lewis <antony@cosmologist.info>
Date: Wed, 21 Aug 2024 16:05:08 +0100
Subject: [PATCH 1/7] add pypi deploy

---
 .github/workflows/tests.yml | 56 +++++++++++++++++++++++++++++--------
 1 file changed, 44 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 2d580f54..0ac23b55 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -1,4 +1,4 @@
-name: CI
+name: Cobaya Tests
 
 # for the moment only runs on "action* branches". Coverage/pypi not yet set up.
 
@@ -23,17 +23,21 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - name: "Anaconda: jammy LTS Python (fast; pip CAMB)"
+          - name: "Anaconda Python (fast; pip CAMB)"
             os: ubuntu-latest
             pydist: "ANACONDA"
-          - name: "Latest Python 3.12"
+          - name: "Latest Python 3.x"
             os: ubuntu-latest
-            python-version: 3.12
+            python-version: 3.x
             mpi: openmpi
-          - name: "OS X Python 3.8"
+            env:
+              COBAYA_INSTALL_SKIP: planck_2015,CamSpec2021,2018_highl_CamSpec,unbinned,keck,classy
+          - name: "OS X Python 3.8 with classy"
             os: macos-latest
             python-version: 3.8
             mpi: openmpi
+            env:
+              COBAYA_INSTALL_SKIP: polychord,planck_2015,CamSpec2021,2018_highl_CamSpec,unbinned,keck
           - name: "Windows Python 3.12"
             os: windows-latest
             python-version: 3.12
@@ -62,6 +66,14 @@ jobs:
         activate-environment: tests-environment
         environment-file: tests-environment.yml
 
+    - name: flake8 Lint
+      if: matrix.pydist == 'ANACONDA'
+      uses: py-actions/flake8@v2
+      with:
+          args: --select=E713,E704,E703,E714,E10,E11,E20,E22,E23,E25,E27,E301,E302,E304,E9,F405,F406,F5,F6,F7,F8,W1,W2,W3,W6 --show-source --statistics
+          path: cobaya
+          max-line-length: "90"
+
     - name: Install mpi
       if: matrix.pydist != 'ANACONDA'
       uses: mpi4py/setup-mpi@v1
@@ -83,12 +95,7 @@ jobs:
       if: matrix.pydist != 'ANACONDA'
       run: |
         pip install mpi4py -i https://pypi.anaconda.org/mpi4py/simple
-        pip install -r requirements.txt pytest-xdist pytest-cov flaky matplotlib dill coverage flake8 iminuit numba camb
-
-    - name: Run flake8
-      shell: bash -el {0}
-      run: |
-        flake8 cobaya --select=E713,E704,E703,E714,E741,E10,E11,E20,E22,E23,E25,E27,E301,E302,E304,E9,F405,F406,F5,F6,F7,F8,W1,W2,W3,W6 --show-source --statistics
+        pip install -r requirements.txt pytest-xdist pytest-cov flaky matplotlib dill coverage iminuit numba camb
 
     - name: Run cobaya install and tests
       shell: bash -el {0}
@@ -111,6 +118,31 @@ jobs:
         coverage run --parallel-mode -m unittest test_package.tests.test
 
 #    - name: Upload coverage to Codecov
-#      uses: codecov/codecov-action@v1
+#      uses: codecov/codecov-action@v4
+#      with:
+#          token: ${{ secrets.CODECOV_TOKEN }}
+
+
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    if: github.repository_owner == 'CobayaSampler' && github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
+    permissions:
+      id-token: write
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+
+    - name: Install dependencies
+      run: |
+        python -m pip install -U pip
+        python -m pip install -U build twine
 
+    - name: Build package
+      run: python -m build --sdist
 
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@release/v1
\ No newline at end of file

From 23292ea01efed8afb8283673fa89b0c04cc17d4e Mon Sep 17 00:00:00 2001
From: Antony Lewis <antony@cosmologist.info>
Date: Wed, 21 Aug 2024 16:43:55 +0100
Subject: [PATCH 2/7] fix and clean

---
 .github/workflows/tests.yml                   | 204 +++++++++---------
 .travis.yml                                   | 153 -------------
 CHANGELOG.md                                  |   4 +-
 DEVEL.rst                                     |   4 +-
 README.rst                                    |   4 +-
 .../likelihoods/base_classes/planck_clik.py   |   2 +-
 tests/common.py                               |   4 +-
 tests/common_sampler.py                       |   4 +-
 tests/test_cosmo_planck_2015.py               |   2 +-
 tests/test_cosmo_planck_2018.py               |   2 +-
 10 files changed, 115 insertions(+), 268 deletions(-)
 delete mode 100644 .travis.yml

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 0ac23b55..871a6868 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -2,125 +2,125 @@ name: Cobaya Tests
 
 # for the moment only runs on "action* branches". Coverage/pypi not yet set up.
 
-on:
-  push:
-    branches:
-      - 'action*'
-    tags:
-      - '*'
-  pull_request:
-    branches:
-      - '*'
+on: [ push, pull_request ]
 
 env:
   COBAYA_INSTALL_SKIP: polychord,planck_2015,CamSpec2021,2018_highl_CamSpec,unbinned,keck,classy
   COBAYA_PACKAGES_PATH: ../packages
 
 jobs:
-  build:
+  tests:
     runs-on: ${{ matrix.os }}
+    if: (github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != 'CobayaSampler/cobaya')
     strategy:
       fail-fast: false
       matrix:
         include:
-          - name: "Anaconda Python (fast; pip CAMB)"
+          - name: "Anaconda Python (flake8, no numba)"
             os: ubuntu-latest
             pydist: "ANACONDA"
-          - name: "Latest Python 3.x"
+          - name: "Latest Python 3.x (with polychord)"
             os: ubuntu-latest
             python-version: 3.x
             mpi: openmpi
             env:
               COBAYA_INSTALL_SKIP: planck_2015,CamSpec2021,2018_highl_CamSpec,unbinned,keck,classy
-          - name: "OS X Python 3.8 with classy"
+            if: !startsWith(github.ref_name, 'test')
+          - name: "OS X Python 3.8 (with classy)"
             os: macos-latest
             python-version: 3.8
             mpi: openmpi
             env:
               COBAYA_INSTALL_SKIP: polychord,planck_2015,CamSpec2021,2018_highl_CamSpec,unbinned,keck
+            if: !startsWith(github.ref_name, 'test')
           - name: "Windows Python 3.12"
             os: windows-latest
             python-version: 3.12
             mpi: intelmpi
+            if: !startsWith(github.ref_name, 'test')
     steps:
-    - run: ln -s $(which gfortran-14) /usr/local/bin/gfortran
-      if: matrix.os == 'macos-latest'
-
-    - run: gfortran --version
-
-    - uses: actions/checkout@v4
-      with:
-        fetch-depth: 0
-
-    - name: Set up Python ${{ matrix.python-version }}
-      if: matrix.pydist != 'ANACONDA'
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Set up Miniconda
-      if: matrix.pydist == 'ANACONDA'
-      uses: conda-incubator/setup-miniconda@v3
-      with:
-        auto-activate-base: false
-        activate-environment: tests-environment
-        environment-file: tests-environment.yml
-
-    - name: flake8 Lint
-      if: matrix.pydist == 'ANACONDA'
-      uses: py-actions/flake8@v2
-      with:
-          args: --select=E713,E704,E703,E714,E10,E11,E20,E22,E23,E25,E27,E301,E302,E304,E9,F405,F406,F5,F6,F7,F8,W1,W2,W3,W6 --show-source --statistics
-          path: cobaya
-          max-line-length: "90"
-
-    - name: Install mpi
-      if: matrix.pydist != 'ANACONDA'
-      uses: mpi4py/setup-mpi@v1
-      with:
-        mpi: ${{ matrix.mpi }}
-
-#    - name: Cache dependencies
-#      uses: actions/cache@v2
-#      with:
-#        path: |
-#          ${{ github.workspace }}/packages/data/planck_supp_data_and_covmats
-#          ${{ github.workspace }}/packages/data/bao_data
-#          ${{ github.workspace }}/packages/data/sn_data
-#          ${{ github.workspace }}/packages/data/des_data
-#          ${{ github.workspace }}/packages/data/planck_2018_pliklite_native
-#        key: ${{ runner.os }}-build-${{ matrix.python-version }}}
-
-    - name: Install dependencies (pip)
-      if: matrix.pydist != 'ANACONDA'
-      run: |
-        pip install mpi4py -i https://pypi.anaconda.org/mpi4py/simple
-        pip install -r requirements.txt pytest-xdist pytest-cov flaky matplotlib dill coverage iminuit numba camb
-
-    - name: Run cobaya install and tests
-      shell: bash -el {0}
-      run: |
-        coverage run --parallel-mode -m cobaya.install polychord --debug
-        coverage run --parallel-mode -m pytest tests/ -n auto -k "not cosmo" --skip-not-installed --no-flaky-report
-        coverage run --parallel-mode -m cobaya.install cosmo-tests --no-progress-bars --debug --skip-global
-        pytest tests/ --cov -vv -s -k "cosmo" -n 2 --skip-not-installed --no-flaky-report
-
-    - name: Run MPI tests
-      shell: bash -el {0}
-      run: |
-        mpiexec -np 2 coverage run --parallel-mode -m pytest -x -m mpi tests/ --no-flaky-report
-
-    - name: Run external likelihood tests
-      shell: bash -el {0}
-      run: |
-        git clone --depth=1 https://github.com/CobayaSampler/example_external_likelihood
-        pip install ./example_external_likelihood --quiet
-        coverage run --parallel-mode -m unittest test_package.tests.test
-
-#    - name: Upload coverage to Codecov
-#      uses: codecov/codecov-action@v4
-#      with:
-#          token: ${{ secrets.CODECOV_TOKEN }}
+      - run: ln -s $(which gfortran-14) /usr/local/bin/gfortran
+        if: matrix.os == 'macos-latest'
+
+      - run: gfortran --version
+
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python ${{ matrix.python-version }}
+        if: matrix.pydist != 'ANACONDA'
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Set up Miniconda
+        if: matrix.pydist == 'ANACONDA'
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-activate-base: false
+          activate-environment: tests-environment
+          environment-file: tests-environment.yml
+
+      - name: flake8 Lint
+        if: matrix.pydist == 'ANACONDA'
+        shell: bash -el {0}
+        run: |
+          flake8 cobaya --max-line-length 90 --select=E713,E704,E703,E714,E10,E11,E20,E22,E23,E25,E27,E301,E302,E304,E9,F405,F406,F5,F6,F7,F8,W1,W2,W3,W6 --show-source --statistics
+
+      - name: Install dependencies (pip)
+        if: matrix.pydist != 'ANACONDA'
+        run: |
+          pip install -r requirements.txt pytest-xdist pytest-cov flaky matplotlib coverage iminuit numba camb
+
+      - name: Install mpi
+        if: matrix.pydist != 'ANACONDA' && matrix.os != 'windows-latest'
+        uses: mpi4py/setup-mpi@v1
+        with:
+          mpi: ${{ matrix.mpi }}
+
+      - name: Install mpi4py
+        if: matrix.pydist != 'ANACONDA' && matrix.os != 'windows-latest'
+        run: |
+          pip install mpi4py -i https://pypi.anaconda.org/mpi4py/simple
+
+      #    - name: Cache dependencies
+      #      uses: actions/cache@v2
+      #      with:
+      #        path: |
+      #          ${{ github.workspace }}/packages/data/planck_supp_data_and_covmats
+      #          ${{ github.workspace }}/packages/data/bao_data
+      #          ${{ github.workspace }}/packages/data/sn_data
+      #          ${{ github.workspace }}/packages/data/des_data
+      #          ${{ github.workspace }}/packages/data/planck_2018_pliklite_native
+      #        key: ${{ runner.os }}-build-${{ matrix.python-version }}}
+
+
+      - name: Run cobaya install and tests
+        shell: bash -el {0}
+        run: |
+          coverage run --parallel-mode -m cobaya.install polychord --debug
+          coverage run --parallel-mode -m pytest tests/ -n auto -k "not cosmo" --skip-not-installed --no-flaky-report
+          coverage run --parallel-mode -m cobaya.install cosmo-tests --no-progress-bars --debug --skip-global
+          pytest tests/ --cov -vv -s -k "cosmo" -n 2 --skip-not-installed --no-flaky-report
+
+      - name: Run MPI tests
+        if: matrix.os != 'windows-latest'
+        shell: bash -el {0}
+        run: |
+          mpiexec -np 2 --oversubscribe coverage run --parallel-mode -m pytest -m mpi tests/ --no-flaky-report
+
+      - name: Run external likelihood tests
+        shell: bash -el {0}
+        run: |
+          git clone --depth=1 https://github.com/CobayaSampler/example_external_likelihood
+          pip install ./example_external_likelihood --quiet
+          coverage run --parallel-mode -m unittest test_package.tests.test
+
+  #    - name: Upload coverage to Codecov
+  #      uses: codecov/codecov-action@v4
+  #      with:
+  #          token: ${{ secrets.CODECOV_TOKEN }}
 
 
   deploy:
@@ -131,18 +131,18 @@ jobs:
       id-token: write
 
     steps:
-    - uses: actions/checkout@v4
+      - uses: actions/checkout@v4
 
-    - name: Set up Python
-      uses: actions/setup-python@v5
+      - name: Set up Python
+        uses: actions/setup-python@v5
 
-    - name: Install dependencies
-      run: |
-        python -m pip install -U pip
-        python -m pip install -U build twine
+      - name: Install dependencies
+        run: |
+          python -m pip install -U pip
+          python -m pip install -U build twine
 
-    - name: Build package
-      run: python -m build --sdist
+      - name: Build package
+        run: python -m build --sdist
 
-    - name: Publish package
-      uses: pypa/gh-action-pypi-publish@release/v1
\ No newline at end of file
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@release/v1
\ No newline at end of file
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index 34442254..00000000
--- a/.travis.yml
+++ /dev/null
@@ -1,153 +0,0 @@
-language: python
-os: linux
-git:
-  depth: false
-
-#testing
-env:
-  global:
-    - COBAYA_INSTALL_SKIP=polychord,planck_2015,CamSpec2021,2018_highl_CamSpec,unbinned,keck
-
-if: (type = pull_request) OR (branch = master) OR (branch =~ ^test.*) OR (branch =~ ^alltest.*) OR (tag IS present)
-
-#Large CamSpec folders tend to hang, so exclude non-base likelihoods from cache
-cache:
-  directories:
-    - /home/travis/build/CosmoPars/packages/code
-    - /home/travis/build/CosmoPars/packages/data/planck_supp_data_and_covmats
-    - /home/travis/build/CosmoPars/packages/data/planck_2018/baseline
-    - /home/travis/build/CosmoPars/packages/data/bicep_keck_2018
-    - /home/travis/build/CosmoPars/packages/data/bao_data
-    - /home/travis/build/CosmoPars/packages/data/sn_data
-    - /home/travis/build/CosmoPars/packages/data/des_data
-    - /home/travis/build/CosmoPars/packages/data/planck_2018_pliklite_native
-
-# (Pre)Installation
-jobs:
-  include:
-    - if: branch !~ ^test.*
-      dist: focal
-      name: "Minimum requisites for dependencies: gcc-7, Python 3.8"
-      addons:
-        apt:
-          packages:
-            - gcc-7
-            - g++-7
-            - gfortran-7
-      env:
-        - GCC_VERSION="7"
-      python: "3.8"
-    - if: branch !~ ^test.*
-      name: "Typical scenario: latest Ubuntu LTS"
-      dist: jammy
-      addons:
-        apt:
-          packages:
-            - gfortran
-      install:
-        - pip install -r requirements.txt camb
-      env:
-        - GCC_VERSION="ubuntu"
-      python: "3.10"
-    - name: "Anaconda: jammy LTS Python (fast; pip CAMB)"
-      dist: jammy
-      env:
-        - GCC_VERSION="ubuntu"
-        - PYDIST="ANACONDA"
-        - ANACONDA_CHANNEL="defaults"
-        - COBAYA_INSTALL_SKIP="$COBAYA_INSTALL_SKIP,classy"
-      language: minimal
-    - if: branch !~ ^test.*
-      name: "Latest jammy Python 3.12"
-      dist: jammy
-      addons:
-        apt:
-          packages:
-            - gfortran
-      env:
-        - GCC_VERSION="ubuntu"
-        - COBAYA_INSTALL_SKIP="$COBAYA_INSTALL_SKIP,classy"
-      python: "3.12"
-
-
-before_install:
-  # Configure right compiler versions
-  - if [[ "$GCC_VERSION" != "ubuntu" ]]; then
-    mkdir -p gcc-symlinks;
-    ln -s /usr/bin/gfortran-$GCC_VERSION gcc-symlinks/gfortran;
-    ln -s /usr/bin/gcc-$GCC_VERSION gcc-symlinks/gcc;
-    ln -s /usr/bin/g++-$GCC_VERSION gcc-symlinks/g++;
-    export PATH=$PWD/gcc-symlinks:$PATH;
-    fi
-  - which gfortran >/dev/null 2>&1 && gfortran --version || echo "gfortran not installed"
-  # Install rest of system requisites
-  # - sudo apt install openmpi-bin openmpi-common libopenmpi-dev libopenblas-dev liblapack-dev
-  # Python requisites
-  - if [[ "$PYDIST" == "ANACONDA" ]]; then
-    wget -q https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-    bash miniconda.sh -b -p $HOME/miniconda;
-    export PATH="$HOME/miniconda/bin:$PATH";
-    hash -r;
-    conda config --set always_yes yes --set changeps1 no;
-    conda info -a;
-    conda create -q -n test-environment -c $ANACONDA_CHANNEL scipy matplotlib cython PyYAML dill coverage pytest pandas;
-    source activate test-environment;
-    conda install -c conda-forge mpi4py openmpi iminuit;
-    pip install -r requirements.txt flake8 flaky pytest-xdist pytest-cov camb;
-    else
-    python -m pip install --upgrade pip setuptools wheel;
-    pip install openmpi mpi4py -i https://pypi.anaconda.org/mpi4py/simple;
-    pip install pytest-xdist pytest-cov flaky matplotlib dill coverage flake8 iminuit numba;
-    fi
-  - python --version
-
-script:
-  # Find undeclared references and syntax errors, plus standardize whitespace etc;
-  # See https://pycodestyle.pycqa.org/en/latest/intro.html#error-codes
-  - flake8 cobaya --select=E713,E704,E703,E714,E741,E10,E11,E20,E22,E23,E25,E27,E301,E302,E304,E9,F405,F406,F5,F6,F7,F8,W1,W2,W3,W6 --show-source --statistics
-  # General tests:
-  - export COBAYA_PACKAGES_PATH="../packages"
-  - coverage run --parallel-mode -m cobaya.install polychord --debug
-  - coverage run --parallel-mode -m pytest tests/ -n auto -k "not cosmo" --skip-not-installed --no-flaky-report
-  # Cosmology tests:
-  - coverage run --parallel-mode -m cobaya.install cosmo-tests --no-progress-bars --debug --skip-global
-  - if [ -n "${CAMB_BRANCH}" ]; then
-    rm -rf $COBAYA_PACKAGES_PATH/code/CAMB ;
-    git clone --recursive --depth 1 -b $CAMB_BRANCH https://github.com/cmbant/CAMB $COBAYA_PACKAGES_PATH/code/CAMB ;
-    python $COBAYA_PACKAGES_PATH/code/CAMB/setup.py build ;
-    fi
-  # mpi tests
-  - mpiexec -np 2 --mca orte_base_help_aggregate 0 --mca btl ^openib --oversubscribe coverage run --parallel-mode -m pytest -x -m mpi tests/ --no-flaky-report ;
-  - mkdir covers; mv .coverage.* covers; ls -ltra covers
-  - pytest tests/ --cov -vv -s -k "cosmo" -n 1 --skip-not-installed --no-flaky-report
-  - mv .coverage .coverage.pytest; mv covers/.cov* .
-  # Test external cosmological likelihoods
-  #- pip install -e $COBAYA_PACKAGES_PATH/code/CAMB --quiet
-  #- git clone --depth=1 https://github.com/CobayaSampler/planck_lensing_external
-  #- pip install ./planck_lensing_external --quiet
-  #- coverage run --parallel-mode -m unittest plancklensing.tests.test_likes
-  - git clone --depth=1 https://github.com/CobayaSampler/example_external_likelihood
-  - pip install ./example_external_likelihood --quiet
-  - coverage run --parallel-mode -m unittest test_package.tests.test
-
-after_success:
-  - bash <(curl -s https://codecov.io/bash)
-
-###############################################################################
-# DEPLOYMENT to PyPI (only if it builds and if the commit has been tagged)
-deploy:
-  provider: pypi
-  on:
-    tags: true
-    python: '3.10'
-    branch: master
-    repo: CobayaSampler/cobaya
-###############################################################################
-  edge: true
-  username: "__token__"
-  password:
-    secure: rSeqVE21XQnzKbY5bjvDgKofhxdoBOSQ+4h7tU+/HaCPNThTYpXD2vfJgtU+y+9ONoGm0l1665JwcIpajP3O8ruFI79ahD773qisgjukIwvO/pHhLsA8othdNAS4f7nOCBVScVMa92UNYpFFHZ6Kom2eJDLLLfqBJxYNfvAn7sPfetHfuYUe55YMF806xf+2ounXBYjHLZFw9V2iks0OVS3gQOSZYuPUn4oPCV32jojD3ZdYIz6tEDigLG9L+dbrzYfg7tOFkXW4OCpDhgB9XIuIrVcfM2oBByI5AmN0gUwBV2i77T3TjoIL6a+Ea0Y6Gn3lgGtgWVHxC6UGVu8uq6+iUc9+NmkRaJu0+kSLRQNb6AJFx+a+xdI2kMw27hy+S/mOzPowJMLcSjtBEjuuvmSFQzdzwldzFfZL5mYBwKdlLl1O/vca9RTaj+FouQyq6NHngBJ2ifhyuLclgyv35F2Ych13dPSToIIid3oJiDCnUHowcQtaUMqiPJW64tY8hbWMriGd9JgggwKg13Zr3bmsyOI4eh8VQG36OyMNEUYuJVJCuOrFtY8AZrs+/6YLqt2WCs3Mboz84ZgfE4d1cch1HQJzLlUOwW14b05XXfXER/iTylN87BV/q9qieY9q9Zwe3XzbG/TWkyHDXpY+Zm0+4AsZgoOapDSZJKwlUb4=
-notifications:
-  email:
-    recipients:
-      - secure: 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
diff --git a/CHANGELOG.md b/CHANGELOG.md
index fc3bc3cf..97dded7a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -286,9 +286,9 @@
 - Added new fast but more realistic running, resuming and post tests with and without mpi
 - Fixed some randomized test inputs for more reliable running
 - drag: True running test
-- Coverage reporting added to Travis
+- Coverage reporting added
 - More useful traceback and console log when error raised running pytest
-- added COBAYA_DEBUG env variable that can be set to force debug output (e.g. set in travis for failed build rerun)
+- added COBAYA_DEBUG env variable that can be set to force debug output (e.g. set in tests for failed build rerun)
 
 ## 3.0.4 – 2021-03-10
 
diff --git a/DEVEL.rst b/DEVEL.rst
index 6b827e62..4a9de7c2 100644
--- a/DEVEL.rst
+++ b/DEVEL.rst
@@ -10,7 +10,7 @@ This document gathers some notes about the development flow, release checklist,
 ``git`` development model
 -------------------------
 
-* Non-breaking travis-passing latest changes and fixes are in master
+* Non-breaking test-passing latest changes and fixes are in master
 * Development that may break tests is done in temp branches or forks and merged to master once OK
 * Breaking changes developed in separate branches, and merged when releases updated
 * Releases are branched out, and only critical bug fixes are pushed onto them.
@@ -45,7 +45,7 @@ can check most formatting and static errors on the command line using::
 Release checklist
 -----------------
 
-+ Make sure all tests pass in Travis (or the package won't be pushed to PyPI).
++ Make sure all tests pass on GitHub Actions (or the package won't be pushed to PyPI).
 + Make sure everything relevant has been added to the Changelog.
 + Delete old deprecation notices (>=2 versions before)
 + Bump version number in ``__init__.py`` and ``CHANGELOG.md`` (also date)
diff --git a/README.rst b/README.rst
index 0e9b132b..d67f53ba 100644
--- a/README.rst
+++ b/README.rst
@@ -15,8 +15,8 @@
 
 :Installation: ``pip install cobaya --upgrade`` (see the `installation instructions <https://cobaya.readthedocs.io/en/latest/installation.html>`_; in general do *not* clone)
 
-.. image:: https://img.shields.io/travis/com/CobayaSampler/cobaya
-   :target: https://app.travis-ci.com/CobayaSampler/cobaya
+.. image:: https://github.com/CobayaSampler/cobaya/actions/workflows/tests.yml/badge.svg?branch=master
+   :target: https://github.com/CobayaSampler/cobaya/actions
 .. image:: https://readthedocs.org/projects/cobaya/badge/?version=latest
    :target: https://cobaya.readthedocs.org/en/latest
 .. image:: https://codecov.io/gh/CobayaSampler/cobaya/branch/master/graphs/badge.svg
diff --git a/cobaya/likelihoods/base_classes/planck_clik.py b/cobaya/likelihoods/base_classes/planck_clik.py
index 7beee7d5..c3e36f63 100644
--- a/cobaya/likelihoods/base_classes/planck_clik.py
+++ b/cobaya/likelihoods/base_classes/planck_clik.py
@@ -235,7 +235,7 @@ def install(cls, path=None, force=False, code=True, data=True,
 common_path = "planck"
 
 # To see full clik build output even if installs OK (e.g. to check warnings)
-_clik_verbose = any((s in os.getenv('TRAVIS_COMMIT_MESSAGE', ''))
+_clik_verbose = any((s in os.getenv('COMMIT_MESSAGE', ''))
                     for s in ["clik", "planck"])
 # Don't try again to install clik if it failed for a previous likelihood
 _clik_install_failed = False
diff --git a/tests/common.py b/tests/common.py
index fc3f8b6b..fd7a1181 100644
--- a/tests/common.py
+++ b/tests/common.py
@@ -4,8 +4,8 @@
 from contextlib import contextmanager
 
 
-def is_travis():
-    return os.environ.get('TRAVIS') == 'true'
+def is_ci_test():
+    return os.environ.get('GITHUB_ACTIONS') == 'true'
 
 
 def process_packages_path(packages_path) -> str:
diff --git a/tests/common_sampler.py b/tests/common_sampler.py
index 01af5ad4..036b832e 100644
--- a/tests/common_sampler.py
+++ b/tests/common_sampler.py
@@ -9,7 +9,7 @@
 from cobaya.typing import InputDict, SamplersDict
 from cobaya.tools import KL_norm
 from cobaya.run import run
-from .common import process_packages_path, is_travis
+from .common import process_packages_path, is_ci_test
 from .conftest import install_test_wrapper
 from cobaya import mpi
 
@@ -96,7 +96,7 @@ def body_of_sampler_test(info_sampler: SamplersDict, dimension=1, n_modes=1, tmp
                 collection["sample"].to_getdist(label="cluster %d" % (i + 1))
                 for i, collection in products["clusters"].items()]
         # Plots!
-        if do_plots and not is_travis():
+        if do_plots and not is_ci_test():
             try:
                 import getdist.plots as gdplots
                 from getdist.gaussian_mixtures import MixtureND
diff --git a/tests/test_cosmo_planck_2015.py b/tests/test_cosmo_planck_2015.py
index 1a521e16..613a24fe 100644
--- a/tests/test_cosmo_planck_2015.py
+++ b/tests/test_cosmo_planck_2015.py
@@ -4,7 +4,7 @@
 from .common_cosmo import body_of_test
 from cobaya.cosmo_input import planck_precision
 
-# Generating plots in Travis
+# Generating plots in tests
 import matplotlib
 
 matplotlib.use('agg')
diff --git a/tests/test_cosmo_planck_2018.py b/tests/test_cosmo_planck_2018.py
index 09e391c4..57d62ad9 100644
--- a/tests/test_cosmo_planck_2018.py
+++ b/tests/test_cosmo_planck_2018.py
@@ -4,7 +4,7 @@
 from .common_cosmo import body_of_test
 from cobaya.cosmo_input import planck_precision
 
-# Generating plots in Travis
+# Generating plots in tests
 try:
     import matplotlib
 

From 35e1973dc8b74d52c42e3ff7932f4b649fa2d62d Mon Sep 17 00:00:00 2001
From: Antony Lewis <antony@cosmologist.info>
Date: Wed, 21 Aug 2024 16:57:42 +0100
Subject: [PATCH 3/7] fix and clean

---
 .github/workflows/tests.yml | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 871a6868..39b5fafd 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -5,7 +5,7 @@ name: Cobaya Tests
 on: [ push, pull_request ]
 
 env:
-  COBAYA_INSTALL_SKIP: polychord,planck_2015,CamSpec2021,2018_highl_CamSpec,unbinned,keck,classy
+  COBAYA_INSTALL_SKIP_BASE: planck_2015,CamSpec2021,2018_highl_CamSpec,unbinned,keck
   COBAYA_PACKAGES_PATH: ../packages
 
 jobs:
@@ -19,30 +19,32 @@ jobs:
           - name: "Anaconda Python (flake8, no numba)"
             os: ubuntu-latest
             pydist: "ANACONDA"
+            cobaya_skip: classy,polychord
           - name: "Latest Python 3.x (with polychord)"
             os: ubuntu-latest
             python-version: 3.x
             mpi: openmpi
-            env:
-              COBAYA_INSTALL_SKIP: planck_2015,CamSpec2021,2018_highl_CamSpec,unbinned,keck,classy
-            if: !startsWith(github.ref_name, 'test')
+            cobaya_skip: classy,polychord
           - name: "OS X Python 3.8 (with classy)"
             os: macos-latest
             python-version: 3.8
             mpi: openmpi
-            env:
-              COBAYA_INSTALL_SKIP: polychord,planck_2015,CamSpec2021,2018_highl_CamSpec,unbinned,keck
-            if: !startsWith(github.ref_name, 'test')
+            cobaya_skip: polychord
           - name: "Windows Python 3.12"
             os: windows-latest
             python-version: 3.12
             mpi: intelmpi
-            if: !startsWith(github.ref_name, 'test')
+            cobaya_skip: classy,polychord
     steps:
+      - name: Set COBAYA_INSTALL_SKIP
+        shell: bash
+        run: echo "COBAYA_INSTALL_SKIP=$COBAYA_INSTALL_SKIP_BASE,${{ matrix.cobaya_skip }}" >> $GITHUB_ENV
+
       - run: ln -s $(which gfortran-14) /usr/local/bin/gfortran
         if: matrix.os == 'macos-latest'
 
-      - run: gfortran --version
+      - run: |
+           gfortran --version
 
       - uses: actions/checkout@v4
         with:
@@ -124,7 +126,7 @@ jobs:
 
 
   deploy:
-    needs: build
+    needs: tests
     runs-on: ubuntu-latest
     if: github.repository_owner == 'CobayaSampler' && github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
     permissions:

From ca0d69230377c3c60e8a2eafd38f8bcb202dd0c9 Mon Sep 17 00:00:00 2001
From: Antony Lewis <antony@cosmologist.info>
Date: Wed, 21 Aug 2024 18:10:48 +0100
Subject: [PATCH 4/7] fix and clean

---
 .github/workflows/tests.yml | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 39b5fafd..aacd282b 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -11,7 +11,7 @@ env:
 jobs:
   tests:
     runs-on: ${{ matrix.os }}
-    if: (github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != 'CobayaSampler/cobaya')
+    if: github.event_name == 'pull_request' || (github.event_name == 'push' && github.event.pull_request == null)
     strategy:
       fail-fast: false
       matrix:
@@ -87,15 +87,12 @@ jobs:
           pip install mpi4py -i https://pypi.anaconda.org/mpi4py/simple
 
       #    - name: Cache dependencies
-      #      uses: actions/cache@v2
+      #      uses: actions/cache@v4
       #      with:
       #        path: |
-      #          ${{ github.workspace }}/packages/data/planck_supp_data_and_covmats
-      #          ${{ github.workspace }}/packages/data/bao_data
-      #          ${{ github.workspace }}/packages/data/sn_data
-      #          ${{ github.workspace }}/packages/data/des_data
-      #          ${{ github.workspace }}/packages/data/planck_2018_pliklite_native
-      #        key: ${{ runner.os }}-build-${{ matrix.python-version }}}
+      #          ${{ env.COBAYA_PACKAGES_PATH }}/data/
+      #        key: ${{ env.COBAYA_INSTALL_SKIP }}
+      #       enableCrossOsArchive: true
 
 
       - name: Run cobaya install and tests

From 16f4e66d1417c4338e67336e959714eea86815da Mon Sep 17 00:00:00 2001
From: Antony Lewis <antony@cosmologist.info>
Date: Wed, 21 Aug 2024 18:23:45 +0100
Subject: [PATCH 5/7] fix and clean

---
 .github/workflows/tests.yml | 28 +++++++++++++++++++++++++++-
 1 file changed, 27 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index aacd282b..0e57c2d2 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -9,9 +9,35 @@ env:
   COBAYA_PACKAGES_PATH: ../packages
 
 jobs:
+  should_run:
+    # only run on pushes that are not also part of PR
+    runs-on: ubuntu-latest
+    outputs:
+      run_tests: ${{ steps.check.outputs.run_tests }}
+    steps:
+      - name: Check if tests should run
+        id: check
+        uses: actions/github-script@v6
+        with:
+          github-token: ${{secrets.GITHUB_TOKEN}}
+          script: |
+            if (context.eventName === 'pull_request') {
+              core.setOutput('run_tests', 'true');
+            } else if (context.eventName === 'push') {
+              const { data: prs } = await github.rest.pulls.list({
+                owner: context.repo.owner,
+                repo: context.repo.repo,
+                head: `${context.repo.owner}:${context.ref.replace('refs/heads/', '')}`,
+                state: 'open'
+              });
+              const shouldRun = prs.length === 0;
+              core.setOutput('run_tests', shouldRun ? 'true' : 'false');
+            }  
+
   tests:
+    needs: should_run
     runs-on: ${{ matrix.os }}
-    if: github.event_name == 'pull_request' || (github.event_name == 'push' && github.event.pull_request == null)
+    if: needs.should_run.outputs.run_tests == 'true'
     strategy:
       fail-fast: false
       matrix:

From 8d6a6366f42d68aaed1c80abeac06bb99d1a4a64 Mon Sep 17 00:00:00 2001
From: Antony Lewis <antony@cosmologist.info>
Date: Wed, 21 Aug 2024 18:26:41 +0100
Subject: [PATCH 6/7] fix and clean

---
 .github/workflows/tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 0e57c2d2..09a3a1f7 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -17,7 +17,7 @@ jobs:
     steps:
       - name: Check if tests should run
         id: check
-        uses: actions/github-script@v6
+        uses: actions/github-script@v7
         with:
           github-token: ${{secrets.GITHUB_TOKEN}}
           script: |

From cdd09e0085c6a915612abbed2dee44aaf5753b99 Mon Sep 17 00:00:00 2001
From: Antony Lewis <antony@cosmologist.info>
Date: Wed, 21 Aug 2024 18:35:43 +0100
Subject: [PATCH 7/7] fix and clean

---
 .github/workflows/tests.yml | 25 +++++++++++--------------
 1 file changed, 11 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 09a3a1f7..03b51108 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -13,31 +13,28 @@ jobs:
     # only run on pushes that are not also part of PR
     runs-on: ubuntu-latest
     outputs:
-      run_tests: ${{ steps.check.outputs.run_tests }}
+      run_tests: github.event_name == 'push' || ${{ steps.check.outputs.run_tests }}
     steps:
       - name: Check if tests should run
         id: check
+        if: github.event_name == 'push'
         uses: actions/github-script@v7
         with:
           github-token: ${{secrets.GITHUB_TOKEN}}
           script: |
-            if (context.eventName === 'pull_request') {
-              core.setOutput('run_tests', 'true');
-            } else if (context.eventName === 'push') {
-              const { data: prs } = await github.rest.pulls.list({
-                owner: context.repo.owner,
-                repo: context.repo.repo,
-                head: `${context.repo.owner}:${context.ref.replace('refs/heads/', '')}`,
-                state: 'open'
-              });
-              const shouldRun = prs.length === 0;
-              core.setOutput('run_tests', shouldRun ? 'true' : 'false');
-            }  
+            const { data: prs } = await github.rest.pulls.list({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              head: `${context.repo.owner}:${context.ref.replace('refs/heads/', '')}`,
+              state: 'open'
+            });
+            const shouldRun = prs.length === 0;
+            core.setOutput('run_tests', shouldRun ? 'true' : 'false');
 
   tests:
     needs: should_run
     runs-on: ${{ matrix.os }}
-    if: needs.should_run.outputs.run_tests == 'true'
+    if: github.event_name == 'pull_request' || needs.should_run.outputs.run_tests == 'true'
     strategy:
       fail-fast: false
       matrix: