Merge branch 'main' into polar-coords

Author: ssagynbayeva

.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

@@ -38,8 +38,8 @@ jobs:
           pip install isort
 
       - name: Install pyro
-        run: python setup.py install --user
+        run: pip install .
 
       - name: Validate
-        run: isort -c pyro
+        run: isort --check --diff 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

@@ -41,8 +41,8 @@ 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
+        run: ./pyro/test.py --nproc 0
 

docs/source/conf.py

@@ -137,6 +137,9 @@
     ]
 }
 
+linkcheck_ignore = [r"https://ascelibrary.org",
+                    r"https://doi.org/10.1061/(ASCE)0733-9429(1999)125:11(1210)"]
+
 
 # -- Options for HTMLHelp output ------------------------------------------
 

docs/source/incompressible_basics.rst

@@ -62,7 +62,18 @@ shown below are run as:
    pyro_sim.py incompressible converge inputs.converge.128 vis.dovis=0
 
 The error is measured by comparing with the analytic solution using
-the routine ``incomp_converge_error.py`` in ``analysis/``.
+the routine ``incomp_converge_error.py`` in ``analysis/``. To generate
+the plot below, run
+
+.. prompt:: bash
+
+   python incompressible/tests/convergence_errors.py convergence_errors.txt
+
+or ``convergence_errors_no_limiter.txt`` after running with that option. Then:
+
+.. prompt:: bash
+
+   python incompressible/tests/convergence_plot.py
 
 .. image:: incomp_converge.png
    :align: center