refactor: misc

* move inline install scripts back to files
* make steps cross-platform where possible
* replace set-output mechanism (soon deprecated)
* test compile on bash, cmd and pwsh on Windows
* save cache after install even if workflow fails
* set env vars for HPC kit, FC and install location
* add conventional commits to README and CONTRIBUTING
* fix cache restore issue on windows
* prepend MSVC linker bindir to system path
* don't use GNU tar on Windows (can't unpack symlinks)
* workaround libimf.so missing issue on Linux
* make install location configurable
* resolve relative paths and expand symlinks

.github/workflows/ci.yml

@@ -8,6 +8,8 @@ on:
     branches:
       - main
       - develop
+env:
+  FC: ifort
 jobs:
   test:
     name: Test
@@ -16,74 +18,67 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest, macos-latest, windows-latest ]
+        path: [ absolute, relative, tilde, default ]
     steps:
       - name: Checkout
         uses: actions/checkout@v3
-      - name: Install ifort
-        uses: ./
-      - name: Test ifort
+      - name: Set bin path
         if: runner.os != 'Windows'
         run: |
-          ./test/test.sh /opt/intel/oneapi
-      - name: Test ifort (Windows)
+          if [ "${{ matrix.path }}" == "absolute" ]; then
+            bindir="$HOME/.local/bin"
+          elif [ "${{ matrix.path }}" == "relative" ]; then
+            bindir="bin"
+          elif [ "${{ matrix.path }}" == "tilde" ]; then
+            bindir="~/.local/bin"
+          else
+            # action's default location
+            bindir="~/.local/bin/ifort"
+          fi
+
+          echo "TEST_BINDIR=$bindir" >> $GITHUB_ENV
+      - name: Set bin path (Windows)
         if: runner.os == 'Windows'
+        shell: pwsh
         run: |
-          ./test/test.ps1 "C:\Program Files (x86)\Intel\oneAPI"
-  test_compile_modflow:
-    name: Test compile modflow6
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ ubuntu-latest, macos-latest, windows-latest ]
-        env: [ pip, miniconda, micromamba ]
-    defaults:
-      run:
-        shell:
-          bash -l {0}
-    steps:
-      - name: Checkout action
-        uses: actions/checkout@v3
-      - name: Checkout modflow6
-        uses: actions/checkout@v3
-        with:
-          repository: MODFLOW-USGS/modflow6
-          path: modflow6
+          if ("${{ matrix.path }}" -eq "absolute") {
+            # $bindir = "C:\Users\runneradmin\.local\bin"
+            $bindir = "C:\Program Files (x86)\Intel\oneAPI"
+          } elseif ("${{ matrix.path }}" -eq "relative") {
+            $bindir = "bin"
+          } elseif ("${{ matrix.path }}" -eq "tilde") {
+            $bindir = "~/.local/bin"
+          } else {
+            # actions's default location
+            $bindir = "~/.local/bin/ifort"
+          }
+
+          echo "TEST_BINDIR=$bindir" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append
       - name: Install ifort
+        if: matrix.path != 'default'
         uses: ./
-      - name: Setup Python
-        if: matrix.env == 'pip'
-        uses: actions/setup-python@v4
-        with:
-          python-version: 3.9
-      - name: Install Python dependencies
-        if: matrix.env == 'pip'
-        run: |
-          pip3 install -r test/requirements.txt
-      - name: Install miniconda environment
-        if: matrix.env == 'miniconda'
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          environment-file: modflow6/environment.yml
-      - name: Install micromamba environment
-        if: matrix.env == 'micromamba'
-        uses: mamba-org/provision-with-micromamba@main
         with:
-          environment-file: modflow6/environment.yml
-          cache-downloads: true
-          cache-env: true
-      - name: Build modflow6
+          path: ${{ env.TEST_BINDIR }}
+      - name: Install ifort
+        if: matrix.path == 'default'
+        uses: ./
+      - name: Test ifort (Linux & Mac)
         if: runner.os != 'Windows'
-        working-directory: modflow6
         run: |
-          meson setup builddir -Ddebug=false --prefix=$(pwd) --libdir=bin
-          meson compile -v -C builddir
-          meson install -C builddir
-      - name: Build modflow6 (Windows)
+          ./test/test.sh ${{ env.TEST_BINDIR }}
+      # TODO: reenable if ifort configuration for bash resolved on Windows
+      # - name: Test ifort (Windows bash)
+      #   if: runner.os == 'Windows'
+      #   shell: bash
+      #   run: |
+      #     ./test/test.sh "${{ env.TEST_BINDIR }}"
+      - name: Test ifort (Windows pwsh)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          ./test/test.ps1 "${{ env.TEST_BINDIR }}"
+      - name: Test ifort (Windows cmd)
         if: runner.os == 'Windows'
-        working-directory: modflow6
+        shell: cmd
         run: |
-          export PATH="/C/Program Files/Microsoft Visual Studio/2022/Enterprise/VC/Tools/MSVC/14.33.31629/bin/Hostx64/x64":$PATH
-          meson setup builddir -Ddebug=false --prefix=$(pwd) --libdir=bin
-          meson compile -v -C builddir
-          meson install -C builddir
+          call "./test/test.bat"

.github/workflows/integration.yml

@@ -0,0 +1,92 @@
+name: MODFLOW 6 integration testing
+on:
+  push:
+    branches:
+      - main
+      - develop
+  pull_request:
+    branches:
+      - main
+      - develop
+  schedule:
+    - cron: '0 6 * * *' # run at 6 AM UTC every day
+jobs:
+  test_build_modflow:
+    name: Test build modflow6
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ ubuntu-latest, macos-latest, windows-latest ]
+        env: [ pip, miniconda, micromamba ]
+    defaults:
+      run:
+        shell:
+          # necessary for miniconda and micromamba
+          # https://github.com/mamba-org/provision-with-micromamba#important
+          bash -l {0}
+    steps:
+      - name: Checkout action
+        uses: actions/checkout@v3
+      - name: Checkout modflow6
+        uses: actions/checkout@v3
+        with:
+          repository: MODFLOW-USGS/modflow6
+          path: modflow6
+      - name: Setup Python
+        if: matrix.env == 'pip'
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+      - name: Install Python dependencies
+        if: matrix.env == 'pip'
+        run: |
+          pip3 install -r test/requirements.txt
+      - name: Install miniconda environment
+        if: matrix.env == 'miniconda'
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          environment-file: modflow6/environment.yml
+      - name: Install micromamba environment
+        if: matrix.env == 'micromamba'
+        uses: mamba-org/provision-with-micromamba@main
+        with:
+          environment-file: modflow6/environment.yml
+          cache-downloads: true
+          cache-env: true
+      - name: Install ifort
+        uses: ./
+        with:
+          path: ${{ runner.os != 'Windows' && 'bin' || 'C:\Program Files (x86)\Intel\oneAPI' }}
+      - name: Build modflow6 (Linux & Mac)
+        if: runner.os != 'Windows'
+        working-directory: modflow6
+        run: |
+          meson setup builddir -Ddebug=false --prefix=$(pwd) --libdir=bin
+          meson compile -v -C builddir
+          meson install -C builddir
+      - name: Add micromamba bindir to path (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          $mamba_bin = "C:\Users\runneradmin\micromamba-root\envs\modflow6\Scripts"
+          if (Test-Path $mamba_bin) {
+            # ifort/micromamba interfere with one another's PATH settings
+            echo $mamba_bin | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
+          }
+      - name: Build modflow6 (Windows pwsh)
+        if: runner.os == 'Windows'
+        working-directory: modflow6
+        shell: pwsh
+        run: |
+          meson setup builddir -Ddebug=false --prefix=$(pwd) --libdir=bin
+          meson compile -v -C builddir
+          meson install -C builddir
+      - name: Build modflow6 (Windows cmd)
+        if: runner.os == 'Windows'
+        working-directory: modflow6
+        shell: cmd /C call {0}
+        run: |
+          meson setup builddir -Ddebug=false --prefix=%CD% --libdir=bin
+          meson compile -v -C builddir
+          meson install -C builddir

CONTRIBUTING.md

@@ -1,3 +1,19 @@
+<!-- START doctoc generated TOC please keep comment here to allow auto update -->
+<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
+**Table of Contents**  *generated with [DocToc](https://github.com/thlorenz/doctoc)*
+
+- [Contributing](#contributing)
+  - [Issues and features](#issues-and-features)
+  - [Pull requests](#pull-requests)
+  - [Commit messages](#commit-messages)
+    - [Commit Message Format](#commit-message-format)
+      - [Type](#type)
+      - [Subject](#subject)
+      - [Body](#body)
+      - [Footer](#footer)
+
+<!-- END doctoc generated TOC please keep comment here to allow auto update -->
+
 # Contributing
 
 Contributions to this repository are welcome. To make a contribution we ask that you follow a few guidelines.
@@ -16,9 +32,11 @@ If `develop` changes while your work is still in progress, please rebase and fix
 
 ## Commit messages
 
-To keep the repository's commit history consistent, commit messages must conform to the following formatting conventions.
+Commit messages must conform to the [conventional commits](https://www.conventionalcommits.org/en/v1.0.0/) specification. This makes the commit history easier to follow and allows an automatically generated changelog.
+
+### Commit Message Format
 
-Each commit message consists of a **header**, a **body** and a **footer**.  The header includes a **type**, a **scope** and a **subject**:
+Each commit message consists of a **header**, a **body** and a **footer**. The **header** is mandatory, while **body** and **footer** are optional.
 
 ```
 <type>(<scope>): <subject>
@@ -28,11 +46,13 @@ Each commit message consists of a **header**, a **body** and a **footer**.  The
 <footer>
 ```
 
-The **header** is mandatory and its **scope** is optional. The message **body** and **footer** are also optional.
+Note the header's format, which includes a **type**, a **scope** and a **subject**. Header **type** and **subject** are mandatory while header **scope** is optional.
+
+No line of the commit message may be longer 100 characters! This makes messages easier to read on GitHub as well as in various `git` tools.
 
-Please keep lines under 100 characters.
+If a commit closes an issue, the footer should contain a [closing reference](https://help.github.com/articles/closing-issues-via-commit-messages/).
 
-### Type
+#### Type
 
 Must be one of the following:
 
@@ -46,33 +66,20 @@ Must be one of the following:
 * **test**: Adding missing tests or correcting existing tests
 * **revert**: Reverts a previous commit
 
-### Scope
-The scope should be the name of the FloPy module/class affected (as perceived by the person reading the changelog generated from commit messages.
-
-There are currently a few exceptions to the "use module/class name" rule:
-
-* **release**: used when updating files prior to a release
-* **releasenotes**: used for updating the release notes
-* **readme**: used for updating the release notes in README.md
-* **changelog**: used for updating the release notes in CHANGELOG.md
-* none/empty string: useful for `style`, `test` and `refactor` changes that are done across all
-  packages (e.g. `style: add missing semicolons`) and for docs changes that are not related to a
-  specific package (e.g. `docs: fix typo in tutorial`).
-
-### Subject
+#### Subject
 
 The subject contains a succinct description of the change:
 
 * use the imperative, present tense: "change" not "changed" nor "changes"
 * don't capitalize the first letter
 * do not include a dot (.) at the end
 
-### Body
+#### Body
 
 Just as in the **subject**, use the imperative, present tense: "change" not "changed" nor "changes".
 The body should include the motivation for the change and contrast this with previous behavior.
 
-### Footer
+#### Footer
 
 The footer should contain any information about **Breaking Changes** and is also the place to reference GitHub issues that this commit **Closes**.