Add builder and GA for pflotran

.github/workflows/full.yml

@@ -0,0 +1,24 @@
+name: Full end-to-end test
+
+on:
+  workflow_dispatch:
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.11"
+    - name: Install dependencies
+      run: pip install .
+    - name: Build environment
+      run: deploy build
+    - name: Test environment
+      run: deploy test
+    - name: Make links
+      run: deploy links

config.yaml

@@ -11,11 +11,19 @@ builds:
       url: https://github.com/petsc/petsc.git
       ref: a093114c2e7b4ba1f47e6ac8a72c57724150f16d
 
+  - name: pflotran
+    version: 1.8.12
+    depends: [ petsc ]
+    src:
+      type: git
+      url: https://bitbucket.org/opengosim/pflotran_ogs_1.8
+      ref: 9dda71eba27f4beef56a269d03037b6f3230578b
+
   - name: runcirrus
     version: 1.0.0
 
 envs:
-  - name: cirrus
+  - name: pflotran
     dest: versions
   - name: runcirrus
     dest: versions/runcirrus

deploy_tests/snapshots/test_cirrus/test_spe1/stdout → deploy_tests/snapshots/test_pflotran/test_spe1/stdout

@@ -1,44 +1,44 @@
- Cirrus was compiled on: [PRUNED]
- RESERVOIR_DEFAULTS keyword selected.
- Cirrus card:: DIMENS                          
- Cirrus card:: EQUALS                          
- Cirrus card:: EQUALS                          
- Cirrus card:: COPY                            
- Cirrus card:: MULTIPLY                        
- Cirrus card:: EQUALS                          
+ Pflotran was compiled on: [PRUNED]
+ RESERVOIR_DEFAULTS option has been selected
+ Pflotran card:: DIMENS                          
+ Pflotran card:: EQUALS                          
+ Pflotran card:: EQUALS                          
+ Pflotran card:: COPY                            
+ Pflotran card:: MULTIPLY                        
+ Pflotran card:: EQUALS                          
  Calculating pore volumes
  Calculating connections
  Ncell=         300  Nact=         300  Nconn=         740  Nflt=           0  Npo=           0
  Reading SUBSURFACE cards:
- Cirrus card:: GRID
- Cirrus card:: TIME
- Cirrus card:: OUTPUT
- Cirrus card:: MATERIAL_PROPERTY
+ Pflotran card:: GRID
+ Pflotran card:: TIME
+ Pflotran card:: OUTPUT
+ Pflotran card:: MATERIAL_PROPERTY
    Name :: formation
- Cirrus card:: CHARACTERISTIC_CURVES
+ Pflotran card:: CHARACTERISTIC_CURVES
    Name :: ch1
- Cirrus card:: EOS
+ Pflotran card:: EOS
  "EOS,WATER,REFERENCE_DENSITY units" set to default value.
  "EOS,WATER,DENSITY,CONSTANT units" set to default value.
  "EOS,WATER,VISCOSITY,CONSTANT units" set to default value.
- Cirrus card:: EOS
+ Pflotran card:: EOS
  "EOS,OIL,FORMULA_WEIGHT units" set to default value.
- Cirrus card:: EOS
+ Pflotran card:: EOS
  "EOS,GAS,FORMULA_WEIGHT units" set to default value.
- Cirrus card:: WELL_DATA
+ Pflotran card:: WELL_DATA
  injg
- Cirrus card:: WELL_DATA
+ Pflotran card:: WELL_DATA
  prod
- Cirrus card:: EQUILIBRATION
+ Pflotran card:: EQUILIBRATION
 
- Cirrus card:: END_SUBSURFACE
+ Pflotran card:: END_SUBSURFACE
  Extent of Gridded Domain
   X: 152.400 - 2895.600
   Y: 152.400 - 2895.600
   Z: -2563.37 - -2543.56
  Created default Region all.
  Requested processors = 1
- Degrees of freedom per cell= 3, number of phases = 3
+ Degrees of freedom per cell= 4, number of phases = 3
 Step   time     tstep    fopt     fopr     fwpr     fgpr     fwir     fgir     fwct     fgor     fpav     NL LI Ch
        days     days     ksm3     sm3/d    sm3/d    ksm3/d   sm3/d    ksm3/d            ksm3/sm3 Bar
 ------ -------- -------- -------- -------- -------- -------- -------- -------- -------- -------- -------- -- -- --

deploy_tests/test_cirrus.py → deploy_tests/test_pflotran.py

@@ -9,20 +9,23 @@
 
 
 def test_help() -> None:
-    output = subprocess.check_output(["cirrus", "-help"])
-    assert b"Cirrus command line options:" in output
+    status = subprocess.run(["pflotran", "-help"], stdout=subprocess.PIPE)
+    assert status.returncode == 87
+    assert b"Options for all PETSc programs:" in status.stdout
 
 
 def test_version() -> None:
-    proc = subprocess.run(["cirrus", "-cirrusin", "/dev/null"], stdout=subprocess.PIPE)
+    proc = subprocess.run(
+        ["pflotran", "-pflotranin", "/dev/null"], stdout=subprocess.PIPE
+    )
 
-    match = re.search(r"Cirrus (\d+\.\d+sv\d+)\n", proc.stdout.decode())
+    match = re.search(r" Pflotran (\d+\.\d+sv\d+)\+\n", proc.stdout.decode())
     assert (
         match
-    ), f"Version not found in the following cirrus output: {proc.stdout.decode()}"
+    ), f"Version not found in the following pflotran output: {proc.stdout.decode()}"
 
     # Get the version as set by `deploy test`
-    version = semver.Version.parse(os.environ["cirrus_version"])
+    version = semver.Version.parse(os.environ["pflotran_version"])
     expected_version = f"{version.major}.{version.minor}sv{version.patch}"
     actual_version = match[1]
 
@@ -32,8 +35,8 @@ def test_version() -> None:
 def test_spe1(tmp_path, snapshot) -> None:
     output = subprocess.check_output(
         [
-            "cirrus",
-            "-cirrusin",
+            "pflotran",
+            "-pflotranin",
             DATADIR / "spe1.in",
             "-output_prefix",
             tmp_path / "spe1",
@@ -45,7 +48,7 @@ def test_spe1(tmp_path, snapshot) -> None:
 
     # Replace strings that change from run to run
     stdout = re.sub(
-        r"(Cirrus was compiled on:|Run completed, wall clock time =).*",
+        r"(Pflotran was compiled on:|Run completed, wall clock time =).*",
         r"\1 [PRUNED]",
         output.decode(),
     )

src/deploy/scripts/build_cirrus.sh → src/deploy/scripts/build_pflotran.sh

@@ -6,22 +6,16 @@ set -ex
 : "${petsc:?}"
 : "${src:?}"
 
-if ! [[ -f "$tmp/six-*-.whl" ]]
-then
-    python3 -m pip download -d "$tmp" six
-fi
-
 # --------------------------------------
-# Build Cirrus
+# Build Pflotran-OGS
 # --------------------------------------
-cd "$src/src/cirrus"
+cd "$src/src/pflotran"
 git reset --hard
 git clean -xdf
 
 export PETSC_DIR="$petsc"
 export PETSC_ARCH=
-export PYTHONPATH="$tmp/six-*-.whl"
 
-make cirrus
-make test
-install -D cirrus "$out/bin/cirrus"
+make UPDATE_PROVENANCE=0 pflotran
+make UPDATE_PROVENANCE=0 check
+install -D pflotran "$out/bin/pflotran"