Restore incremental Cython builds in Makefile

.github/workflows/CI.yml

@@ -77,7 +77,7 @@ jobs:
         shell: bash -l {0}
     steps:
       - name: Checkout RMG-Py
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Setup Miniforge Python ${{ matrix.python-version }}
         uses: conda-incubator/setup-miniconda@v3
@@ -138,7 +138,7 @@ jobs:
         shell: bash -l {0}
     steps:
       - name: Checkout RMG-Py
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Setup Miniforge Python 3.9
         uses: conda-incubator/setup-miniconda@v3

.github/workflows/annotate.yml

@@ -21,7 +21,7 @@ jobs:
     steps:
       - run: echo 'The triggering workflow passed'
       - name: 'Download regression_summary artifact'
-        uses: actions/github-script@v6
+        uses: actions/github-script@v8
         with:
           script: |
             let allArtifacts = await github.rest.actions.listWorkflowRunArtifacts({

.github/workflows/conda_build.yml

@@ -24,7 +24,7 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: Setup Miniforge
         uses: conda-incubator/setup-miniconda@v3
@@ -34,7 +34,7 @@ jobs:
           auto-update-conda: true
           show-channel-urls: true
           conda-remove-defaults: "true"
-          auto-activate-base: "true"
+          auto-activate: true
           activate-environment: ""
 
       - name: Install Build Tools

.github/workflows/docs.yml

@@ -22,7 +22,7 @@ jobs:
           git config --global user.email "github-actions@github.com"
 
       - name: Clone RMG-Py
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
@@ -68,7 +68,7 @@ jobs:
           make
 
       - name: Checkout gh-pages Branch
-        uses: actions/checkout@v2
+        uses: actions/checkout@v6
         with:
           ref: gh-pages
           fetch-depth: 0

.github/workflows/stale.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check for Stale Issues and Pull Requests
-        uses: actions/stale@main
+        uses: actions/stale@v10
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           stale-issue-message: 'This issue is being automatically marked as stale because it has not received any interaction in the last 90 days. Please leave a comment if this is still a relevant issue, otherwise it will automatically be closed in 30 days.'

Makefile

@@ -7,29 +7,49 @@
 CC=gcc
 CXX=g++
 
-.PHONY : all check clean install decython documentation test q2dtor
+# Sentinel file written after a successful pip editable install.
+# Lives in the source tree; deleted by `make clean`.
+INSTALL_SENTINEL = .installed
 
-all: check install check
+.PHONY : all build check clean install decython documentation test q2dtor
+
+# Default target: ensure installed, then build any changed extensions in place.
+all: check $(INSTALL_SENTINEL) build check
 
 check:
 	@ python utilities.py check-dependencies
 	@ python utilities.py check-pydas
 
+define DO_INSTALL
+	@ python utilities.py check-pydas
+	python -m pip install --no-build-isolation -vv -e .
+	@ touch $(INSTALL_SENTINEL)
+endef
+
+# Runs only if the sentinel doesn't exist.
+$(INSTALL_SENTINEL):
+	$(DO_INSTALL)
+
+# Explicit install target
+install:
+	$(DO_INSTALL)
+
+# Incremental in-place build; skips pip entirely.
+build:
+	python setup.py build_ext --inplace
+
 documentation:
 	$(MAKE) -C documentation html
 	@ echo "Start at: documentation/build/html/index.html"
 
 clean:
 	@ python utilities.py clean
 	python -m pip uninstall --yes reactionmechanismgenerator || true  # can fail if RMG not installed at all
+	@ rm -f $(INSTALL_SENTINEL)
 
 clean-solver:
 	@ python utilities.py clean-solver
 
-install:
-	@ python utilities.py check-pydas
-	python -m pip install --no-build-isolation -vv -e .
-
 q2dtor:
 	@ echo -e "\nInstalling Q2DTor...\n"
 	@ echo -e "Q2DTor is a software for calculating the partition functions and themodynamic properties\
@@ -112,7 +132,7 @@ eg7: all
 	cp examples/rmg/gri_mech_rxn_lib/input.py testing/eg7/input.py
 	@ echo "Running eg7: gri_mech_rxn_lib example"
 	python rmg.py testing/eg7/input.py
-	
+
 scoop: all
 	mkdir -p testing/scoop
 	rm -rf testing/scoop/*