More test coverage and other cleanup

.github/PULL_REQUEST_TEMPLATE.md

@@ -31,7 +31,7 @@ Bug fix checklist:
 - [ ] All new and existing tests pass.
 - [ ] I have checked that I reproduce the reference simulations or if there are differences they are explained below (if appropriate). If there are changes that are correct, I will update the reference simulation files after this PR is merged.
 - [ ] I have checked (e.g., using the benchmarking tools) that this change does not significantly increase typical runtimes. If it does, I have included a justification in the comments on this PR.
-- [ ] I have updated the [CHANGELOG](https://github.com/RadioAstronomySoftwareGroup/pyuvsim/blob/master/CHANGELOG.md).
+- [ ] I have updated the [CHANGELOG](https://github.com/RadioAstronomySoftwareGroup/pyuvsim/blob/main/CHANGELOG.md).
 
 New feature checklist:
 - [ ] I have added or updated the docstrings associated with my feature using the [numpy docstring format](https://numpydoc.readthedocs.io/en/latest/format.html).
@@ -40,7 +40,7 @@ New feature checklist:
 - [ ] All new and existing tests pass.
 - [ ] I have checked that I reproduce the reference simulations or if there are differences they are explained below (if appropriate). If there are changes that are correct, I will update the reference simulation files after this PR is merged.
 - [ ] I have checked (e.g., using the benchmarking tools) that this change does not significantly increase typical runtimes. If it does, I have included a justification in the comments on this PR.
-- [ ] I have updated the [CHANGELOG](https://github.com/RadioAstronomySoftwareGroup/pyuvsim/blob/master/CHANGELOG.md).
+- [ ] I have updated the [CHANGELOG](https://github.com/RadioAstronomySoftwareGroup/pyuvsim/blob/main/CHANGELOG.md).
 
 Breaking change checklist:
 - [ ] I have updated the docstrings associated with my change using the [numpy docstring format](https://numpydoc.readthedocs.io/en/latest/format.html).
@@ -50,19 +50,19 @@ Breaking change checklist:
 - [ ] All new and existing tests pass.
 - [ ] I have checked that I reproduce the reference simulations or if there are differences they are explained below (if appropriate). If there are changes that are correct, I will update the reference simulation files after this PR is merged.
 - [ ] I have checked (e.g., using the benchmarking tools) that this change does not significantly increase typical runtimes. If it does, I have included a justification in the comments on this PR.
-- [ ] I have updated the [CHANGELOG](https://github.com/RadioAstronomySoftwareGroup/pyuvsim/blob/master/CHANGELOG.md).
+- [ ] I have updated the [CHANGELOG](https://github.com/RadioAstronomySoftwareGroup/pyuvsim/blob/main/CHANGELOG.md).
 
 Reference simulation update or replacement:
 - [ ] If this is a new reference simulation or if the settings files have changed, I have added all the relevant files to the reference_simulations folder.
 - [ ] If this is a new reference simulation I have fully documented it in a memo in docs and updated any other docs as appropriate.
-- [ ] I have updated the [CHANGELOG](https://github.com/RadioAstronomySoftwareGroup/pyuvsim/blob/master/CHANGELOG.md).
+- [ ] I have updated the [CHANGELOG](https://github.com/RadioAstronomySoftwareGroup/pyuvsim/blob/main/CHANGELOG.md).
 
 Documentation change checklist:
 - [ ] Any updated docstrings use the [numpy docstring format](https://numpydoc.readthedocs.io/en/latest/format.html).
 - [ ] If this is a significant change to the readme or other docs, I have checked that they are rendered properly on ReadTheDocs. (you may need help to get this branch to build on RTD, just ask!)
 
 Version change checklist:
-- [ ] I have updated the [CHANGELOG](https://github.com/RadioAstronomySoftwareGroup/pyuvsim/blob/master/CHANGELOG.md) to put all the unreleased changes under the new version (leaving the unreleased section empty).
+- [ ] I have updated the [CHANGELOG](https://github.com/RadioAstronomySoftwareGroup/pyuvsim/blob/main/CHANGELOG.md) to put all the unreleased changes under the new version (leaving the unreleased section empty).
 - [ ] I have run the appropriate tests for this level of version change (described in the readme under versioning).
 
 Build or continuous integration change checklist:

.github/workflows/testsuite.yaml

@@ -63,54 +63,51 @@ jobs:
           env_vars: OS,PYTHON
           fail_ci_if_error: true
 
+  # Use pip for diversity
+  # do this on min_deps because it's hard to get mpi4py to install from pip
   min_deps:
     env:
-      ENV_NAME: min_deps
-      PYTHON: 3.9
+      PYTHON: "3.10"
     name: Min Deps Testing
-    defaults:
-      run:
-        # Adding -l {0} helps ensure conda can be found properly.
-        shell: bash -l {0}
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@main
         with:
-          fetch-depth: 1
-      - name: Setup Minimamba
-        uses: conda-incubator/setup-miniconda@v2
+          fetch-depth: 0
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
         with:
-          miniforge-variant: Mambaforge
-          miniforge-version: latest
-          use-mamba: true
           python-version: ${{ env.PYTHON }}
-          environment-file: ci/${{ env.ENV_NAME }}.yaml
-          activate-environment: ${{ env.ENV_NAME }}
 
-      - name: Conda Info
+      # need to install the testing packages but not the other optional ones
+      - name: Install
         run: |
-          conda info -a
-          conda list
+          pip install coverage pytest pytest-cov pytest-xdist
+          pip install -e .
+
+      - name: Environment Info
+        run: |
+          pip list
           PYVER=`python -c "import sys; print('{:d}.{:d}'.format(sys.version_info.major, sys.version_info.minor))"`
           if [[ $PYVER != ${{ env.PYTHON }} ]]; then
             exit 1;
           fi
 
-      - name: Install
+      - name: Run Tests
         run: |
-          pip install --no-deps .
+          python -m pytest -n auto --cov=pyuvsim --cov-config=.coveragerc --cov-report xml:./coverage.xml
 
-      - name: Run Tests
+      - name: check coverage report
         run: |
-          python -m pytest -n auto --cov=pyuvsim --cov-config=.coveragerc --cov-report xml:./coverage.xml --junitxml=test-reports/xunit.xml
+          ls
+          cat coverage.xml
 
       - uses: codecov/codecov-action@v3
         if: success()
         with:
           token: ${{secrets.CODECOV_TOKEN}} #required
-          file: ./coverage.xml #optional
-          env_vars: OS,PYTHON
-          fail_ci_if_error: true
+          files: ./coverage.xml #optional
 
   min_versions:
     env:

README.md

@@ -1,7 +1,7 @@
 # pyuvsim
 
-![](https://github.com/RadioAstronomySoftwareGroup/pyuvsim/workflows/Tests/badge.svg?branch=master)
-[![codecov](https://codecov.io/gh/RadioAstronomySoftwareGroup/pyuvsim/branch/master/graph/badge.svg)](https://codecov.io/gh/RadioAstronomySoftwareGroup/pyuvsim)
+![](https://github.com/RadioAstronomySoftwareGroup/pyuvsim/workflows/Tests/badge.svg?branch=main)
+[![codecov](https://codecov.io/gh/RadioAstronomySoftwareGroup/pyuvsim/branch/main/graph/badge.svg)](https://codecov.io/gh/RadioAstronomySoftwareGroup/pyuvsim)
 
 pyuvsim is a comprehensive simulation package for radio interferometers in python.
 

docs/conf.py

@@ -46,6 +46,7 @@
     'sphinx.ext.mathjax',
     'sphinx.ext.viewcode',
     "sphinx.ext.intersphinx",
+    "sphinx_rtd_theme",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -79,12 +80,7 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-# html_theme = 'alabaster
-html_theme = "default"
-html_theme_options = {
-    "rightsidebar": "false",
-    "relbarbgcolor": "black"
-}
+html_theme = "sphinx_rtd_theme"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -166,6 +162,7 @@
 napoleon_custom_sections = [("Attributes", "params_style")]
 autodoc_typehints = 'signature'
 
+
 def build_custom_docs(app):
     sys.path.append(os.getcwd())
     import make_index

docs/developers.rst

@@ -26,7 +26,7 @@ More information on checking the reference simulations can be found in the READM
 
 We will periodically issue a new set of reference simulations as ``pyuvsim`` gains more capabilities.
 
-For more details, see `reference_simulations/README.md <https://github.com/RadioAstronomySoftwareGroup/pyuvsim/tree/master/reference_simulations>`_.
+For more details, see `reference_simulations/README.md <https://github.com/RadioAstronomySoftwareGroup/pyuvsim/tree/main/reference_simulations>`_.
 
 Benchmarking
 ------------
@@ -37,4 +37,4 @@ The README file in the ``benchmarking`` directory gives more details on how to d
 
 Note that the benchmarking scripts are designed only for SLURM systems.
 
-For more details, see `benchmarking/README.md <https://github.com/RadioAstronomySoftwareGroup/pyuvsim/tree/master/benchmarking>`_.
+For more details, see `benchmarking/README.md <https://github.com/RadioAstronomySoftwareGroup/pyuvsim/tree/main/benchmarking>`_.

pyuvsim/branch_scheme.py

@@ -14,7 +14,7 @@ def branch_scheme(version):  # pragma: nocover
     if version.exact or version.node is None:
         return version.format_choice("", "+d{time:{time_format}}", time_format="%Y%m%d")
     else:
-        if version.branch == "master":
+        if version.branch == "main":
             return version.format_choice("+{node}", "+{node}.dirty")
         else:
             return version.format_choice("+{node}.{branch}", "+{node}.{branch}.dirty")

pyuvsim/tests/test_simsetup.py

@@ -267,11 +267,15 @@ def test_mock_diffuse_maps(modname, modkwargs, hera_loc, apollo_loc, location):
 @pytest.mark.filterwarnings("ignore:The lst_array is not self-consistent")
 @pytest.mark.filterwarnings("ignore:Telescope Triangle is not in known_telescopes.")
 @pytest.mark.parametrize(
-    ("horizon_buffer", "pass_time", "pass_uv", "return_catname"),
-    [(True, True, False, None), (False, False, True, False), (True, True, True, False)]
+    ("horizon_buffer", "pass_time", "pass_array_loc", "pass_uv", "return_catname"),
+    [
+        (True, True, True, False, None),
+        (False, False, False, True, False),
+        (True, True, True, True, False)
+    ]
 )
 def test_initialize_catalog_from_params(
-    horizon_buffer, pass_time, pass_uv, return_catname, hera_loc
+    horizon_buffer, pass_time, pass_array_loc, pass_uv, return_catname, hera_loc
 ):
     # Pass in parameter dictionary as dict
     uv_in = UVData.from_file(triangle_uvfits_file)
@@ -285,6 +289,11 @@ def test_initialize_catalog_from_params(
     if horizon_buffer:
         source_dict["horizon_buffer"] = 0.04364
 
+    if pass_array_loc:
+        source_dict["array_location"] = ",".join(
+            [str(coord) for coord in uv_in.telescope_location_lat_lon_alt_degrees]
+        )
+
     warn_type = []
     warn_str = []
     if pass_time:
@@ -297,8 +306,9 @@ def test_initialize_catalog_from_params(
         uv_use = uv_in
     else:
         uv_use = None
-        warn_type += [UserWarning]
-        warn_str += ["No array_location specified. Defaulting to the HERA site."]
+        if not pass_array_loc:
+            warn_type += [UserWarning]
+            warn_str += ["No array_location specified. Defaulting to the HERA site."]
 
     if return_catname is None:
         warn_type += [DeprecationWarning]
@@ -424,7 +434,8 @@ def test_gleam_catalog(filetype, flux_cut):
 
 
 @pytest.mark.parametrize("use_filetype", [True, False])
-def test_skyh5_catalog(use_filetype, tmp_path):
+@pytest.mark.parametrize("yaml_filetype", [True, False])
+def test_skyh5_catalog(use_filetype, yaml_filetype, tmp_path):
     filetype = None
     gleam_filename = os.path.join(
         SIM_DATA_PATH, 'gleam_50srcs.vot'
@@ -447,6 +458,8 @@ def test_skyh5_catalog(use_filetype, tmp_path):
         param_dict = yaml.safe_load(yf)
 
     param_dict['sources']['catalog'] = skyh5_file
+    if yaml_filetype:
+        param_dict['sources']['filetype'] = "skyh5"
     with open(param_filename, 'w') as yfile:
         yaml.dump(param_dict, yfile, default_flow_style=False)