Change MFC version to 5.1.0 and update dependencies

.github/workflows/bottle.yml

@@ -2,11 +2,6 @@ name: Bottle
 
 on:
   push:
-    branches:
-      - main
-    paths:
-      - "Formula/**"
-      - ".github/workflows/bottle.yml"
   workflow_dispatch:
 
 permissions:
@@ -30,31 +25,28 @@ jobs:
       - name: Set up Homebrew
         uses: Homebrew/actions/setup-homebrew@master
 
+      # IMPORTANT: do NOT untap mflowcode/mfc in this job. setup-homebrew manages it and
+      # its post-cleanup expects the tap directory to exist.
+      - name: Ensure no leftover local tap
+        shell: bash
+        run: |
+          set -euo pipefail
+          brew untap mflowcode/local >/dev/null 2>&1 || true
+
       - name: Determine version and root URL (from checked-out formula)
         id: meta
+        shell: bash
         run: |
           set -euo pipefail
-
           FORMULA="Formula/mfc.rb"
-
-          # Take the *last* matching URL (guards against accidental duplicates)
           URL="$(
-            grep -E '^\s*url\s+"https://github.com/.*/archive/refs/tags/v[0-9]+\.[0-9]+\.[0-9]+\.tar\.gz"' "${FORMULA}" \
-              | sed -E 's/^\s*url\s+"([^"]+)".*/\1/' \
+            grep -Eo 'https://github.com/[^"]+/archive/refs/tags/v[0-9]+\.[0-9]+\.[0-9]+\.tar\.gz' "${FORMULA}" \
               | tail -n 1
           )"
-
-          if [[ -z "${URL}" ]]; then
-            echo "Could not extract release tarball URL from ${FORMULA}" >&2
-            echo "Expected a line like: url \"https://github.com/<org>/<repo>/archive/refs/tags/vX.Y.Z.tar.gz\"" >&2
-            exit 1
-          fi
+          [[ -n "${URL}" ]]
 
           VERSION="$(echo "${URL}" | sed -E 's/.*v([0-9]+\.[0-9]+\.[0-9]+)\.tar\.gz/\1/')"
-          if [[ -z "${VERSION}" ]]; then
-            echo "Could not parse version from URL: ${URL}" >&2
-            exit 1
-          fi
+          [[ -n "${VERSION}" ]]
 
           TAG="mfc-${VERSION}"
           ROOT_URL="https://github.com/${GITHUB_REPOSITORY}/releases/download/${TAG}"
@@ -68,74 +60,68 @@ jobs:
           echo "Release tag:      ${TAG}"
           echo "Bottle root_url:  ${ROOT_URL}"
 
-      - name: Install formula with --build-bottle (from checked-out formula via temp tap)
+      - name: Install formula with --build-bottle (tap formula)
+        shell: bash
         run: |
           set -euo pipefail
-
-          echo "Installing mfc with --build-bottle from checked-out Formula/mfc.rb via a temporary local tap..."
-
-          # brew tap-new needs git identity sometimes
-          git config --global user.email "github-actions[bot]@users.noreply.github.com"
-          git config --global user.name "github-actions[bot]"
-
-          # Create a local tap and copy the formula into Homebrew's tap location
-          brew tap-new mflowcode/local
-          TAP_DIR="$(brew --repository)/Library/Taps/mflowcode/homebrew-local"
-          mkdir -p "${TAP_DIR}/Formula"
-          cp Formula/mfc.rb "${TAP_DIR}/Formula/mfc.rb"
-
-          # Homebrew may exit non-zero due to dylib fixup issues in Python wheels,
-          # even though the formula actually installed correctly. Treat that as
-          # non-fatal as long as the formula is present.
+          echo "Installing mfc with --build-bottle (allowing non-fatal dylib fixup failures)..."
+
           set +e
-          brew install --build-bottle mflowcode/local/mfc 2>&1 | tee /tmp/brew-install.log
+          brew install --build-bottle mflowcode/mfc/mfc 2>&1 | tee /tmp/brew-install.log
           brew_exit_code=$?
           set -e
-      
-          if brew list mfc &>/dev/null; then
+
+          if brew list mflowcode/mfc/mfc &>/dev/null; then
             echo "✅ mfc installed successfully (ignoring dylib fixup warnings)"
           else
             echo "❌ mfc installation failed; propagating brew exit code"
             exit $brew_exit_code
           fi
 
       - name: Run Sod shock tube test case
+        shell: bash
         run: |
           set -euo pipefail
           echo "Running a simple test case (1D Sod shock tube) on ${{ matrix.os }}..."
-
-          TESTDIR=$(mktemp -d)
-          cp "$(brew --prefix mfc)/examples/1D_sodshocktube/case.py" "$TESTDIR/"
-
+          TESTDIR="$(mktemp -d)"
+          cp "$(brew --prefix mflowcode/mfc/mfc)/examples/1D_sodshocktube/case.py" "$TESTDIR/"
           cd "$TESTDIR"
           mfc case.py -j 1
-
           test -d "$TESTDIR/silo_hdf5"
           echo "✅ Test case ran successfully and produced output"
 
       - name: Basic installation verification
+        shell: bash
         run: |
           set -euo pipefail
+          PREFIX="$(brew --prefix mflowcode/mfc/mfc)"
+
           echo "1. Checking binaries..."
-          test -x "$(brew --prefix mfc)/bin/pre_process"
-          test -x "$(brew --prefix mfc)/bin/simulation"
-          test -x "$(brew --prefix mfc)/bin/post_process"
-          test -x "$(brew --prefix mfc)/bin/mfc"
+          test -x "${PREFIX}/bin/pre_process"
+          test -x "${PREFIX}/bin/simulation"
+          test -x "${PREFIX}/bin/post_process"
+          test -x "${PREFIX}/bin/mfc"
+
           echo "2. Checking toolchain..."
-          test -d "$(brew --prefix mfc)/toolchain"
+          test -d "${PREFIX}/toolchain"
+
           echo "3. Checking Python venv..."
-          test -d "$(brew --prefix mfc)/libexec/venv"
-          test -x "$(brew --prefix mfc)/libexec/venv/bin/python"
+          test -d "${PREFIX}/libexec/venv"
+          test -x "${PREFIX}/libexec/venv/bin/python"
+
           echo "4. Checking examples..."
-          test -d "$(brew --prefix mfc)/examples"
+          test -d "${PREFIX}/examples"
+
           echo "5. Testing mfc command..."
           mfc --help
+
           echo "✅ All verification checks passed on ${{ matrix.os }}"
 
-      - name: Build bottle
+      - name: Build bottle (tap formula)
+        shell: bash
         run: |
           set -euo pipefail
-          brew bottle --root-url="${{ steps.meta.outputs.root_url }}" --json mfc
+          brew bottle --root-url="${{ steps.meta.outputs.root_url }}" --json mflowcode/mfc/mfc
           ls -1 *.bottle.*
 
       - name: Upload bottle artifacts
@@ -161,125 +147,107 @@ jobs:
 
       - name: Determine version and root URL (from checked-out formula)
         id: meta
+        shell: bash
         run: |
           set -euo pipefail
-
           FORMULA="Formula/mfc.rb"
-
           URL="$(
-            grep -E '^\s*url\s+"https://github.com/.*/archive/refs/tags/v[0-9]+\.[0-9]+\.[0-9]+\.tar\.gz"' "${FORMULA}" \
-              | sed -E 's/^\s*url\s+"([^"]+)".*/\1/' \
+            grep -Eo 'https://github.com/[^"]+/archive/refs/tags/v[0-9]+\.[0-9]+\.[0-9]+\.tar\.gz' "${FORMULA}" \
               | tail -n 1
           )"
-
-          if [[ -z "${URL}" ]]; then
-            echo "Could not extract release tarball URL from ${FORMULA}" >&2
-            exit 1
-          fi
-
+          [[ -n "${URL}" ]]
+
           VERSION="$(echo "${URL}" | sed -E 's/.*v([0-9]+\.[0-9]+\.[0-9]+)\.tar\.gz/\1/')"
-          if [[ -z "${VERSION}" ]]; then
-            echo "Could not parse version from URL: ${URL}" >&2
-            exit 1
-          fi
-
+          [[ -n "${VERSION}" ]]
+
           TAG="mfc-${VERSION}"
           ROOT_URL="https://github.com/${GITHUB_REPOSITORY}/releases/download/${TAG}"
-      
+
           echo "version=${VERSION}" >> "$GITHUB_OUTPUT"
           echo "tag=${TAG}" >> "$GITHUB_OUTPUT"
           echo "root_url=${ROOT_URL}" >> "$GITHUB_OUTPUT"
 
+      - name: Configure git for bottle merge
+        shell: bash
+        run: |
+          set -euo pipefail
+          git config --global user.email "github-actions[bot]@users.noreply.github.com"
+          git config --global user.name "github-actions[bot]"
+
       - name: Download all bottle artifacts
         uses: actions/download-artifact@v4
         with:
           path: bottles
 
       - name: Flatten bottle directory
+        shell: bash
         run: |
           set -euo pipefail
           echo "Before flattening:"
           find bottles -name '*.bottle.*' -type f
-
           find bottles -mindepth 2 -name '*.bottle.*' -type f -exec mv {} bottles/ \;
-
           echo ""
           echo "After flattening:"
           ls -1 bottles/*.bottle.*
 
       - name: Rename bottles for GitHub release
+        shell: bash
         run: |
           set -euo pipefail
           echo "Renaming bottles (mfc-- → mfc-)..."
-
           for file in bottles/mfc--*.bottle.*; do
             if [[ -f "$file" ]]; then
               newname=$(echo "$file" | sed 's/mfc--/mfc-/')
               mv "$file" "$newname"
               echo "  $file → $newname"
             fi
           done
-
           echo ""
           echo "Bottles ready for upload:"
           ls -1 bottles/*.bottle.*
 
       - name: Merge bottle metadata into formula
         id: merge
+        shell: bash
         run: |
           set -euo pipefail
-
+          shopt -s nullglob
           JSON_BOTTLES=(bottles/*.bottle*.json)
-          if [[ ! -e "${JSON_BOTTLES[0]}" ]]; then
+          if (( ${#JSON_BOTTLES[@]} == 0 )); then
             echo "No bottle metadata (*.bottle*.json) found in bottles/"
             ls -la bottles/
             exit 1
           fi
-
+      
           echo "Merging bottle metadata from:"
           printf '%s\n' "${JSON_BOTTLES[@]}"
-
-          BEFORE_SHA=$(git rev-parse HEAD)
-          echo "HEAD before merge: ${BEFORE_SHA}"
-
-          brew bottle --merge --write "${JSON_BOTTLES[@]}"
-
-          AFTER_SHA=$(git rev-parse HEAD)
-          echo "HEAD after merge: ${AFTER_SHA}"
-
+
+          BEFORE_SHA="$(git rev-parse HEAD)"
+          brew bottle --merge --write --root-url="${{ steps.meta.outputs.root_url }}" "${JSON_BOTTLES[@]}"
+          AFTER_SHA="$(git rev-parse HEAD)"
+
           if [[ "${BEFORE_SHA}" != "${AFTER_SHA}" ]]; then
-            echo "✅ New bottle commit created by brew bottle --write"
+            echo "✅ brew bottle --write created commit ${AFTER_SHA}"
             echo "bottle_updated=true" >> "$GITHUB_OUTPUT"
           else
-            echo "ℹ️  No new commit (bottles unchanged or already present)"
+            echo "ℹ️  No commit created (bottles unchanged or already present)"
             echo "bottle_updated=false" >> "$GITHUB_OUTPUT"
           fi
 
       - name: Push bottle updates if changed
         if: steps.merge.outputs.bottle_updated == 'true'
+        shell: bash
         run: |
           set -euo pipefail
-
-          echo "Pushing bottle update commit..."
-          git log -1 --stat
-
-          git config --local --unset-all http.https://github.com/.extraheader || true
-          git remote set-url origin https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/${{ github.repository }}.git
-
+          git remote set-url origin "https://x-access-token:${{ github.token }}@github.com/${{ github.repository }}.git"
           git push origin HEAD:main
 
-      - name: Create or update GitHub Release
+      - name: Create/update release and upload bottles
         uses: softprops/action-gh-release@v1
         with:
           tag_name: ${{ steps.meta.outputs.tag }}
           name: MFC bottles ${{ steps.meta.outputs.version }}
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Upload bottles to Release
-        uses: softprops/action-gh-release@v1
-        with:
-          tag_name: ${{ steps.meta.outputs.tag }}
           files: bottles/*.bottle.*
+          fail_on_unmatched_files: true
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ github.token }}

Formula/mfc.rb

@@ -29,13 +29,11 @@ def install
     # Create Python virtual environment inside libexec (inside Cellar for proper bottling)
     venv = libexec/"venv"
     system Formula["python@3.12"].opt_bin/"python3.12", "-m", "venv", venv
-
     system venv/"bin/pip", "install", "--upgrade",
            "pip", "setuptools", "wheel",
            "setuptools-scm",
            "hatchling", "hatch-vcs",
            "editables"
-
     # Install Cantera from PyPI using pre-built wheel (complex package, doesn't need custom flags)
     # Cantera has CMake compatibility issues when building from source with newer CMake versions
     # Match the version constraint from toolchain/pyproject.toml
@@ -47,8 +45,9 @@ def install
     # Keep toolchain in buildpath for now - mfc.sh needs it there
     #
     # MFC's toolchain uses VCS-derived versioning (via Hatch/hatch-vcs) and Homebrew builds from
-    # GitHub release tarballs without a .git directory. Scope pretend-version env vars tightly
-    # to avoid polluting subsequent pip installs.
+    # GitHub release tarballs without a .git directory. Use --no-build-isolation so the build
+    # backend can see our environment variables, and set SETUPTOOLS_SCM_PRETEND_VERSION which
+    # hatch-vcs respects when VCS metadata is unavailable.
     pretend_env = {
       "SETUPTOOLS_SCM_PRETEND_VERSION_FOR_MFC" => version.to_s,
       "SETUPTOOLS_SCM_PRETEND_VERSION_FOR_mfc" => version.to_s,
@@ -61,7 +60,7 @@ def install
     end
 
     begin
-      system venv/"bin/pip", "install", "-e", buildpath/"toolchain"
+      system venv/"bin/pip", "install", "--no-build-isolation", "-e", buildpath/"toolchain"
     ensure
       pretend_env.each_key do |k|
         if saved_env[k].nil?
@@ -79,7 +78,12 @@ def install
     # Now build MFC with pre-configured venv
     # Set VIRTUAL_ENV so mfc.sh uses existing venv instead of creating new one
     ENV["VIRTUAL_ENV"] = venv
-
+
+    # Also set pretend-version env vars for mfc.sh in case it tries to reinstall toolchain
+    ENV["SETUPTOOLS_SCM_PRETEND_VERSION_FOR_MFC"] = version.to_s
+    ENV["SETUPTOOLS_SCM_PRETEND_VERSION_FOR_mfc"] = version.to_s
+    ENV["SETUPTOOLS_SCM_PRETEND_VERSION"] = version.to_s
+
     # Build MFC using pre-configured venv
     # Must run from buildpath (MFC root directory) where toolchain/ exists
     Dir.chdir(buildpath) do