From ee48a48f47185e17c567515b43d3f43257352ae7 Mon Sep 17 00:00:00 2001
From: jtyoung84 <104453205+jtyoung84@users.noreply.github.com>
Date: Fri, 2 Aug 2024 14:05:07 -0700
Subject: [PATCH 1/2] ci: updates github actions (#99)

* ci: updates github actions
---
 .github/workflows/publish_main.yml            |  94 ++++++++++++
 .../{test_and_lint.yml => run_dev_tests.yml}  |   4 +-
 .github/workflows/run_main_tests.yml          |  43 ++++++
 .github/workflows/tag_and_publish.yml         | 138 ------------------
 4 files changed, 139 insertions(+), 140 deletions(-)
 create mode 100644 .github/workflows/publish_main.yml
 rename .github/workflows/{test_and_lint.yml => run_dev_tests.yml} (94%)
 create mode 100644 .github/workflows/run_main_tests.yml
 delete mode 100644 .github/workflows/tag_and_publish.yml

diff --git a/.github/workflows/publish_main.yml b/.github/workflows/publish_main.yml
new file mode 100644
index 00000000..a8ab1c98
--- /dev/null
+++ b/.github/workflows/publish_main.yml
@@ -0,0 +1,94 @@
+name: Tag and publish main
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  tag_and_publish:
+    name: Parse version
+    runs-on: ubuntu-latest
+    outputs:
+      pkg_version: ${{ steps.output_version.outputs.pkg_version }}
+    steps:
+    - uses: actions/checkout@v3
+    - name: Get version from file
+      run: |
+        pkg_name=$(grep -P 'version = \{attr = .*\}' pyproject.toml | grep -oP '\w+.__version__')
+        init_file="./src/${pkg_name//.__version__}/__init__.py"
+        pkg_version=$(grep -Po '[0-9]+\.[0-9]+\.[0-9]+' "$init_file")
+        echo "tag=$pkg_version" >> "$GITHUB_ENV"
+    - name: Create git tag
+      run: |
+        git tag "v${{ env.tag }}"
+    - name: Push git tag
+      run: git push origin "v${{ env.tag }}"
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.10'
+    - name: Install dependencies
+      run: |
+        pip install --upgrade setuptools wheel twine build
+        python -m build
+        twine check dist/*
+    - name: Publish on PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        password: ${{ secrets.AIND_PYPI_TOKEN }}
+  publish_container:
+    runs-on: ubuntu-latest
+    env:
+      GO_VERSION: '1.14.12'
+      GO_OS: 'linux'
+      GO_ARCH: 'amd64'
+      SINGULARITY_VERSION: '3.7.0'
+    steps:
+      - uses: actions/checkout@v3
+      - name: Get version from file
+        run: |
+          pkg_name=$(grep -P 'version = \{attr = .*\}' pyproject.toml | grep -oP '\w+.__version__')
+          init_file="./src/${pkg_name//.__version__}/__init__.py"
+          pkg_version=$(grep -Po '[0-9]+\.[0-9]+\.[0-9]+' "$init_file")
+          echo "tag=$pkg_version" >> "$GITHUB_ENV"
+      - name: Install dependencies
+        run: |
+          sudo apt-get update && sudo apt-get install -y \
+          build-essential \
+          libssl-dev \
+          uuid-dev \
+          libgpgme11-dev \
+          squashfs-tools \
+          libseccomp-dev \
+          wget \
+          pkg-config \
+          procps
+      - name: Install GO
+        run: |
+          wget https://dl.google.com/go/go$GO_VERSION.$GO_OS-$GO_ARCH.tar.gz
+          sudo tar -C /usr/local -xzvf go$GO_VERSION.$GO_OS-$GO_ARCH.tar.gz
+          sudo rm go$GO_VERSION.$GO_OS-$GO_ARCH.tar.gz
+          echo 'export PATH=$PATH:/usr/local/go/bin' | sudo tee -a /etc/profile
+      - name: Install Singularity
+        run: |
+          cd ..
+          wget https://github.com/hpcng/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-${SINGULARITY_VERSION}.tar.gz
+          sudo tar -xzf singularity-${SINGULARITY_VERSION}.tar.gz
+          sudo rm singularity-${SINGULARITY_VERSION}.tar.gz
+          echo "Finished installing binaries"
+          export PATH=$PATH:/usr/local/go/bin
+          cd singularity
+          sudo ./mconfig --without-suid
+          sudo make -C ./builddir
+          sudo make -C ./builddir install
+      - name: Build sif container
+        run: |
+          ls /
+          ls
+          mkdir build
+          sudo singularity build build/container.sif scripts/singularity_build.def
+      - name: Login and Deploy Container
+        run: |
+          echo ${{ secrets.GITHUB_TOKEN }} | singularity remote login -u ${{ github.actor }} --password-stdin oras://ghcr.io
+          singularity push build/container.sif oras://ghcr.io/${GITHUB_REPOSITORY}:${{ env.tag }}
+          singularity push build/container.sif oras://ghcr.io/${GITHUB_REPOSITORY}:latest
diff --git a/.github/workflows/test_and_lint.yml b/.github/workflows/run_dev_tests.yml
similarity index 94%
rename from .github/workflows/test_and_lint.yml
rename to .github/workflows/run_dev_tests.yml
index 33ef8a9f..a5a1a187 100644
--- a/.github/workflows/test_and_lint.yml
+++ b/.github/workflows/run_dev_tests.yml
@@ -1,9 +1,9 @@
-name: Lint and run tests
+name: Run checks in dev
 
 on:
   pull_request:
     branches:
-      - main
+      - dev
 
 jobs:
   ci:
diff --git a/.github/workflows/run_main_tests.yml b/.github/workflows/run_main_tests.yml
new file mode 100644
index 00000000..eb3b2b66
--- /dev/null
+++ b/.github/workflows/run_main_tests.yml
@@ -0,0 +1,43 @@
+name: Run checks in main and release
+
+on:
+  pull_request:
+    branches:
+      - '*release*'
+      - main
+
+jobs:
+  ci:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ '3.10', '3.11' ]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: | 
+        python -m pip install -e .[dev]
+    - name: Run linter checks
+      run: flake8 . && interrogate --verbose .
+    - name: Run tests and coverage
+      run: coverage run -m unittest discover && coverage report
+  verify_version:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Check version incremented
+        run: |
+          pkg_name=$(grep -P 'version = \{attr = .*\}' pyproject.toml | grep -oP '\w+.__version__')
+          init_file="./src/${pkg_name//.__version__}/__init__.py"
+          pkg_version=$(grep -Po '[0-9]+\.[0-9]+\.[0-9]+' "$init_file")
+          latest_tag=$(git ls-remote --tags --refs --sort="v:refname" | tail -n1 | sed 's/.*\///')
+          echo "Checking pkg_version v$pkg_version and latest_tag $latest_tag"
+          if [ "$latest_tag" == "v$pkg_version" ]
+          then
+            exit 1
+          fi
+          echo "Versions are different"
diff --git a/.github/workflows/tag_and_publish.yml b/.github/workflows/tag_and_publish.yml
deleted file mode 100644
index 2e67be3b..00000000
--- a/.github/workflows/tag_and_publish.yml
+++ /dev/null
@@ -1,138 +0,0 @@
-name: Tag and publish
-on:
-  push:
-    branches:
-      - main
-jobs:
-  update_badges:
-    runs-on: ubuntu-latest
-    continue-on-error: true
-    steps:
-    - uses: actions/checkout@v3
-      with:
-        ref: ${{ env.DEFAULT_BRANCH }}
-        fetch-depth: 0
-        token: ${{ secrets.SERVICE_TOKEN }}
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v3
-      with:
-        python-version: '3.10'
-    - name: Install dependencies
-      run: | 
-        python -m pip install -e .[dev] --no-cache-dir
-    - name: Get Python version and Update README.md
-      run: |
-        python_version=$(grep "requires-python" pyproject.toml | grep -o ">=[^\"]*")
-        python_badge=$(grep -o 'python-[^)]*' README.md)
-        new_python_badge="python-$python_version-blue?logo=python"
-        sed -i "s/$python_badge/$new_python_badge/g" README.md
-    - name: Get interrogate values and Update README.md
-      run: |
-        interrogate_val=$(interrogate . | grep -o 'actual: [0-9]*\.[0-9]*' | awk '{print $2}')
-        interrogate_badge=$(grep -o 'interrogate-[^)]*' README.md)
-        if (( $(echo "$interrogate_val >= 90.00" | bc -l) )); then
-            new_interrogate_badge="interrogate-$interrogate_val%25-brightgreen"
-        elif (( $(echo "$interrogate_val < 80.00" | bc -l) )); then
-            new_interrogate_badge="interrogate-$interrogate_val%25-red"
-        else
-            new_interrogate_badge="interrogate-$interrogate_val%25-yellow"
-        fi
-        sed -i "s/$interrogate_badge/$new_interrogate_badge/g" README.md
-    - name: Get Coverage values and Update README.md
-      run: |
-        coverage run -m unittest discover
-        coverage_val=$(coverage report | grep "^TOTAL" | grep -o '[0-9]\+%' | grep -o '[0-9]\+')
-        coverage_badge=$(grep -o "coverage-[^?]*" README.md)
-        if (( $(echo "$coverage_val >= 90.00" | bc -l) )); then 
-            new_coverage_badge="coverage-$coverage_val%25-brightgreen"
-        elif (( $(echo "$coverage_val < 80.00" | bc -l) )); then
-            new_coverage_badge="coverage-$coverage_val%25-red"
-        else
-            new_coverage_badge="coverage-$coverage_val%25-yellow"
-        fi
-        sed -i "s/$coverage_badge/$new_coverage_badge/g" README.md
-    - name: Commit changes
-      uses: EndBug/add-and-commit@v9
-      with:
-        default_author: github_actions
-        message: "ci: update badges [skip actions]"
-        add: '["README.md"]'
-  tag:
-    needs: update_badges
-    uses: AllenNeuralDynamics/aind-github-actions/.github/workflows/tag.yml@main
-    secrets:
-      SERVICE_TOKEN: ${{ secrets.SERVICE_TOKEN }}
-  publish:
-    needs: tag
-    if: true
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - name: Pull latest changes
-        run: git pull origin main
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v2
-        with:
-          python-version: '3.10'
-      - name: Install dependencies
-        run: |
-          pip install --upgrade setuptools wheel twine build
-          python -m build
-          twine check dist/*
-      - name: Publish on PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          password: ${{ secrets.AIND_PYPI_TOKEN }}
-  publish_container:
-    runs-on: ubuntu-latest
-    env:
-      GO_VERSION: '1.14.12'
-      GO_OS: 'linux'
-      GO_ARCH: 'amd64'
-      SINGULARITY_VERSION: '3.7.0'
-    needs: tag
-    steps:
-      - uses: actions/checkout@v3
-      - name: Pull latest changes
-        run: git pull origin main
-      - name: Install dependencies
-        run: |
-          sudo apt-get update && sudo apt-get install -y \
-          build-essential \
-          libssl-dev \
-          uuid-dev \
-          libgpgme11-dev \
-          squashfs-tools \
-          libseccomp-dev \
-          wget \
-          pkg-config \
-          procps
-      - name: Install GO
-        run: |
-          wget https://dl.google.com/go/go$GO_VERSION.$GO_OS-$GO_ARCH.tar.gz
-          sudo tar -C /usr/local -xzvf go$GO_VERSION.$GO_OS-$GO_ARCH.tar.gz
-          sudo rm go$GO_VERSION.$GO_OS-$GO_ARCH.tar.gz
-          echo 'export PATH=$PATH:/usr/local/go/bin' | sudo tee -a /etc/profile
-      - name: Install Singularity
-        run: |
-          cd ..
-          wget https://github.com/hpcng/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-${SINGULARITY_VERSION}.tar.gz
-          sudo tar -xzf singularity-${SINGULARITY_VERSION}.tar.gz
-          sudo rm singularity-${SINGULARITY_VERSION}.tar.gz
-          echo "Finished installing binaries"
-          export PATH=$PATH:/usr/local/go/bin
-          cd singularity
-          sudo ./mconfig --without-suid
-          sudo make -C ./builddir
-          sudo make -C ./builddir install
-      - name: Build sif container
-        run: |
-          ls /
-          ls
-          mkdir build
-          sudo singularity build build/container.sif scripts/singularity_build.def
-      - name: Login and Deploy Container
-        run: |
-          echo ${{ secrets.GITHUB_TOKEN }} | singularity remote login -u ${{ github.actor }} --password-stdin oras://ghcr.io
-          singularity push build/container.sif oras://ghcr.io/${GITHUB_REPOSITORY}:${{ needs.tag.outputs.new_version }}
-          singularity push build/container.sif oras://ghcr.io/${GITHUB_REPOSITORY}:latest

From 2aa8b3fe59440c08a2889ba8ca0512099f3410f8 Mon Sep 17 00:00:00 2001
From: jtyoung84 <104453205+jtyoung84@users.noreply.github.com>
Date: Fri, 2 Aug 2024 14:07:03 -0700
Subject: [PATCH 2/2] release: v0.14.0

---
 src/aind_metadata_mapper/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/aind_metadata_mapper/__init__.py b/src/aind_metadata_mapper/__init__.py
index 2966b686..77cd89c4 100644
--- a/src/aind_metadata_mapper/__init__.py
+++ b/src/aind_metadata_mapper/__init__.py
@@ -1,3 +1,3 @@
 """Init package"""
 
-__version__ = "0.13.2"
+__version__ = "0.14.0"