From f24f31cb2d7772c6cd4e522d00fa335954ab8498 Mon Sep 17 00:00:00 2001
From: George Dang <53052793+gtdang@users.noreply.github.com>
Date: Thu, 8 Aug 2024 13:03:47 -0400
Subject: [PATCH] Revert "ci: removed other workflows to test only linkcheck."

This reverts commit 1503b84c3426025bd5b7e877bbac02943579fdc4.
---
 .github/workflows/codespell.yml          | 22 ++++++++
 .github/workflows/issue-metrics.yml      | 45 ++++++++++++++++
 .github/workflows/unix_unit_tests.yml    | 68 ++++++++++++++++++++++++
 .github/workflows/windows_unit_tests.yml | 45 ++++++++++++++++
 4 files changed, 180 insertions(+)
 create mode 100644 .github/workflows/codespell.yml
 create mode 100644 .github/workflows/issue-metrics.yml
 create mode 100644 .github/workflows/unix_unit_tests.yml
 create mode 100644 .github/workflows/windows_unit_tests.yml

diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
new file mode 100644
index 000000000..c5e16043e
--- /dev/null
+++ b/.github/workflows/codespell.yml
@@ -0,0 +1,22 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2
diff --git a/.github/workflows/issue-metrics.yml b/.github/workflows/issue-metrics.yml
new file mode 100644
index 000000000..ce7d1ba70
--- /dev/null
+++ b/.github/workflows/issue-metrics.yml
@@ -0,0 +1,45 @@
+name: Monthly issue metrics
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '3 2 1 * *'
+
+permissions:
+  contents: write
+
+jobs:
+  build:
+    name: issue metrics
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: read
+
+    steps:
+
+    - name: Get dates for last month
+      shell: bash
+      run: |
+        # Calculate the first day of the previous month
+        first_day=$(date -d "last month" +%Y-%m-01)
+
+        # Calculate the last day of the previous month
+        last_day=$(date -d "$first_day +1 month -1 day" +%Y-%m-%d)
+
+        #Set an environment variable with the date range
+        echo "$first_day..$last_day"
+        echo "last_month=$first_day..$last_day" >> "$GITHUB_ENV"
+
+    - name: Run issue-metrics tool
+      uses: github/issue-metrics@v3
+      env:
+        GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        SEARCH_QUERY: 'repo:jonescompneurolab/hnn-core is:issue created:${{ env.last_month }}'
+
+    - name: Create issue
+      uses: peter-evans/create-issue-from-file@v4
+      with:
+        title: Monthly issue metrics report
+        token: ${{ secrets.GITHUB_TOKEN }}
+        content-filepath: ./issue_metrics.md
\ No newline at end of file
diff --git a/.github/workflows/unix_unit_tests.yml b/.github/workflows/unix_unit_tests.yml
new file mode 100644
index 000000000..1e6ff5330
--- /dev/null
+++ b/.github/workflows/unix_unit_tests.yml
@@ -0,0 +1,68 @@
+  name: Unit tests
+
+  on:
+    push:
+      branches: ['**']
+    pull_request:
+      branches: ['**']
+
+  jobs:
+    build:
+
+      runs-on: ${{ matrix.os }}
+      strategy:
+        matrix:
+          os: [ubuntu-latest,macos-latest]
+          python-version: [3.8, 3.11, 3.12]
+
+      steps:
+        - uses: actions/checkout@v4
+
+        - name: Install Ubuntu System dependencies
+          if: matrix.os == 'ubuntu-latest'
+          shell: bash -el {0}
+          run: |
+              sudo add-apt-repository ppa:ubuntu-toolchain-r/test
+              sudo apt-get update
+              sudo apt-get install libopenmpi-dev openmpi-bin
+
+        - name: Activate conda environment for macOS
+          if: matrix.os == 'macos-latest'
+          uses: conda-incubator/setup-miniconda@v3
+          with:
+            activate-environment: test
+            python-version: ${{ matrix.python-version }}
+            fetch-depth: 2
+
+        - name: Activate Python environment for Ubuntu
+          if: matrix.os == 'ubuntu-latest'
+          uses: actions/setup-python@v5
+          with:
+              python-version: ${{ matrix.python-version }}
+        
+        - name: Install Python  dependencies
+          shell: bash -el {0}
+          run: |
+            if [ ${{ matrix.os }} == 'macos-latest' ]; then
+              python -m pip install --upgrade pip
+              conda install --yes -c conda-forge mpi4py openmpi
+            elif [[ "${{ matrix.os }}" == "ubuntu-latest" ]]; then 
+              python -m pip install --upgrade pip
+              python -m pip install mpi4py
+            fi
+        - name: Install HNN-core
+          shell: bash -el {0}
+          run: |
+            pip install --verbose '.[opt, parallel, test, gui]'
+        - name: Lint with flake8
+          shell: bash -el {0}
+          run: |
+            flake8 --count hnn_core
+        - name: Test with pytest
+          shell: bash -el {0}
+          run: |
+            python -m pytest ./hnn_core/tests/  --cov=hnn_core --cov-report=xml
+        - name:  Upload coverage to Codecov
+          shell: bash -el {0}
+          run: |
+            bash <(curl -s https://codecov.io/bash) -f ./coverage.xml
\ No newline at end of file
diff --git a/.github/workflows/windows_unit_tests.yml b/.github/workflows/windows_unit_tests.yml
new file mode 100644
index 000000000..e836599fd
--- /dev/null
+++ b/.github/workflows/windows_unit_tests.yml
@@ -0,0 +1,45 @@
+name: Unit test
+
+on:
+  push:
+    branches: ['**']
+  pull_request:
+    branches: ['**']
+
+env:
+    PYTHONPATH: C:\nrn_test\lib\python
+    NEURONHOME: C:\nrn_test
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [windows-latest]
+        python-version: [3.8, 3.11, 3.12]
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: test
+          python-version: ${{ matrix.python-version }}
+      - name: Install Neuron on Windows separately
+        shell: cmd
+        run: |
+          powershell -command "gh release download --repo https://github.com/neuronsimulator/nrn --pattern '*.exe' --output nrn-setup.exe"
+          start /b /wait .\nrn-setup.exe /S /D=C:\nrn_test
+          powershell -command "'C:\nrn_test\bin' >> $env:GITHUB_PATH"
+          python -c "import neuron"
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: Install dependencies and HNN
+        shell: cmd
+        run: |
+          python -m pip install --upgrade pip
+          pip install --verbose .[opt,parallel,test,gui]
+      - name: Test with pytest
+        shell: cmd
+        run: |
+          python -m pytest ./hnn_core/tests/