Pick up new benchmarks automatically and improve github actions (#146)

Add coverage config file and install pyro with pip instead of running setup.py directly

Author: yut23

.coveragerc

@@ -0,0 +1,16 @@
+[paths]
+# files installed in */site-packages/pyro/ are equivalent to those in pyro/
+source =
+  pyro
+  */site-packages/pyro
+
+[run]
+source = pyro
+# measure the source files from the installed pyro package
+source_pkgs = pyro
+
+[report]
+# don't include the test files themselves
+omit =
+  */tests/*
+  pyro/test.py

.github/workflows/docs-test.yml

@@ -38,7 +38,7 @@ jobs:
         run: pip install -r ./requirements.txt
 
       - name: Install pyro
-        run: python setup.py install
+        run: pip install .
 
       - name: Build docs
         run: |

.github/workflows/flake8.yml

@@ -38,7 +38,7 @@ jobs:
           pip install flake8
 
       - name: Install pyro
-        run: python setup.py install --user
+        run: pip install .
 
       - name: Run flake8
         run: flake8 pyro

.github/workflows/gh-pages.yml

@@ -34,7 +34,7 @@ jobs:
         run: pip install -r ./requirements.txt
 
       - name: Install pyro
-        run: python setup.py install
+        run: pip install .
 
       - name: Build docs
         run: ./deploy_docs_action.sh
@@ -44,4 +44,4 @@ jobs:
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: ./out
-          keep_files: true
+          keep_files: true

.github/workflows/isort.yml

@@ -38,7 +38,7 @@ jobs:
           pip install isort
 
       - name: Install pyro
-        run: python setup.py install --user
+        run: pip install .
 
       - name: Validate
         run: isort -c pyro

.github/workflows/pylint.yml

@@ -38,7 +38,7 @@ jobs:
           pip install pylint
 
       - name: Install pyro
-        run: python setup.py install --user
+        run: pip install .
 
       - name: Validate
         run: pylint --errors-only pyro pyro/analysis

.github/workflows/pytest.yml

@@ -41,7 +41,7 @@ jobs:
           pip install -r requirements.txt
 
       - name: Install pyro
-        run: python setup.py install --user
+        run: pip install .
 
       - name: Run tests with pytest
-        run: pytest -v --cov=. --cov-config .coveragerc --nbval --ignore=docs --ignore=./pyro/multigrid/variable_coeff_elliptic.ipynb --ignore=examples/mesh --ignore=examples/multigrid --ignore=presentations
+        run: pytest -v --cov=pyro --nbval --ignore=docs --ignore=./pyro/multigrid/variable_coeff_elliptic.ipynb --ignore=examples/mesh --ignore=examples/multigrid --ignore=presentations

.github/workflows/regtest.yml

@@ -41,7 +41,7 @@ jobs:
           pip install -r requirements.txt
 
       - name: Install pyro
-        run: python setup.py install --user
+        run: pip install .
 
       - name: Run tests via test.py
         run: ./pyro/test.py

setup.py

@@ -19,21 +19,10 @@
     if not f.endswith("inputs.auto"):
         inputs.append(f.replace("pyro/", ""))
 
-benchmarks = ["advection/tests/*.h5",
-              "advection_fv4/tests/*.h5",
-              "advection_nonuniform/tests/*.h5",
-              "advection_rk/tests/*.h5",
-              "compressible/tests/*.h5",
-              "compressible/tests/*.h5",
-              "compressible/tests/*.h5",
-              "compressible_fv4/tests/*.h5",
-              "compressible_rk/tests/*.h5",
-              "compressible_sdc/tests/*.h5",
-              "diffusion/tests/*.h5",
-              "incompressible/tests/*.h5",
-              "lm_atm/tests/*.h5",
-              "multigrid/tests/*.h5",
-              "swe/tests/*.h5"]
+# find all of the benchmark output files
+benchmarks = []
+for path in Path("pyro").glob("*/tests/*.h5"):
+    benchmarks.append(str(path.relative_to("pyro")))
 
 setup(name='pyro-hydro',
       description='A python hydrodynamics code for teaching and prototyping',