Rcal-298: Set Up Testing Infrastructure

.github/workflows/cancel_workflows.yml

@@ -0,0 +1,19 @@
+name: Cancel duplicate workflows
+
+on:
+  workflow_run:
+    workflows: ["CI"]
+    types:
+      - requested
+
+# Note: This has to be in workflow_run so it works for PRs from forks.  And only cancel
+# pull_request triggers, not push, i.e. merges into master.
+jobs:
+  cancel:
+    runs-on: ubuntu-latest
+    if: ${{ github.event.workflow_run.event == 'pull_request' }}
+    steps:
+    - name: Cancel previous runs
+      uses: styfle/[email protected]
+      with:
+        workflow_id: ${{ github.event.workflow.id }}

.github/workflows/ci.yml

@@ -0,0 +1,232 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+      - '*.x'
+    tags:
+      - '*'
+  pull_request:
+    branches:
+      - main
+  schedule:
+    # Weekly Monday 9AM build
+    # * is a special character in YAML so you have to quote this string
+    - cron: '0 9 * * 0'
+
+env:
+  CRDS_SERVER_URL: "https://roman-crds-test.stsci.edu"
+  CRDS_PATH: "/tmp/crds_cache"
+  CRDS_CLIENT_RETRY_COUNT: 3
+  CRDS_CLIENT_RETRY_DELAY_SECONDS: 20
+
+jobs:
+  style:
+    name: Code style checks
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        id: python
+        with:
+          python-version: 3.9
+      - uses: actions/cache@v3
+        with:
+          path: ${{ env.pythonLocation }}
+          key: style-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml', '**/setup.*') }}
+      - run: pip install pyproject-flake8
+      - run: pip freeze
+      - run: flake8
+  audit:
+    name: Bandit security audit
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        id: python
+        with:
+          python-version: 3.9
+      - uses: actions/cache@v3
+        with:
+          path: ${{ env.pythonLocation }}
+          key: audit-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml', '**/setup.*') }}
+      - run: pip install bandit
+      - run: pip freeze
+      - run: bandit romanisim -r -x tests,regtest
+  dependencies:
+    name: verify dependencies are correct
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        id: python
+        with:
+          python-version: 3.9
+      - uses: actions/cache@v3
+        with:
+          path: ${{ env.pythonLocation }}
+          key: dependencies-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml', '**/setup.*') }}
+      - run: pip install .
+      - run: pip freeze
+      - run: verify_install_requires
+  test:
+    name: test
+    needs: [ style, audit, dependencies ]
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ ubuntu-latest, macos-latest ]
+        python: [ 3.8, 3.9, '3.10' ]
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        id: python
+        with:
+          python-version: ${{ matrix.python }}
+      - uses: actions/cache@v3
+        with:
+          path: ${{ env.pythonLocation }}
+          key: test-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml', '**/setup.*') }}
+      - run: pip install ".[test]" pytest-xdist
+      - run: pip freeze
+      - run: pytest -n auto
+  test_alldeps:
+    name: test optional dependencies
+    needs: [ test ]
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ ubuntu-latest, macos-latest ]
+        python: [ 3.8, 3.9, '3.10' ]
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        id: python
+        with:
+          python-version: ${{ matrix.python }}
+      - uses: actions/cache@v3
+        with:
+          path: ${{ env.pythonLocation }}
+          key: test-alldeps-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml', '**/setup.*') }}
+      - run: pip install ".[test,all]" pytest-xdist
+      - run: pip freeze
+      - run: pytest -n auto
+  test_devdeps:
+    name: test developer versions
+    needs: [ test ]
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ ubuntu-latest, macos-latest ]
+        python: [ 3.8, 3.9, '3.10' ]
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        id: python
+        with:
+          python-version: ${{ matrix.python }}
+      - uses: actions/cache@v3
+        with:
+          path: ${{ env.pythonLocation }}
+          key: test-devdeps-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml', '**/setup.*') }}
+      - run: pip install git+https://github.com/asdf-format/asdf git+https://github.com/spacetelescope/stpipe git+https://github.com/spacetelescope/stdatamodels --pre astropy numpy
+      - run: pip install ".[test]" pytest-xdist
+      - run: pip freeze
+      - run: pytest -n auto
+  test_pyargs:
+    name: test --pyargs
+    needs: [ test ]
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ ubuntu-latest, macos-latest ]
+        python: [ 3.8, 3.9, '3.10' ]
+        exclude:
+          - os: macos-latest
+            python: '3.10'
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        id: python
+        with:
+          python-version: ${{ matrix.python }}
+      - uses: actions/cache@v3
+        with:
+          path: ${{ env.pythonLocation }}
+          key: test-pyargs-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml', '**/setup.*') }}
+      - run: pip install ".[test]" pytest-xdist
+      - run: pip freeze
+      - run: pytest -n auto ./docs --pyargs romanisim
+  test_older_numpy:
+    name: test Numpy ${{ matrix.numpy }} (Python ${{ matrix.python }})
+    needs: [ test ]
+    runs-on: ${{ matrix.os }}
+    continue-on-error: true
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ ubuntu-latest ]
+        python: [ 3.8, 3.9, '3.10' ]
+        numpy: [ '1.20.*', '1.21.*', '1.22.*' ]
+        exclude:
+          - python: '3.10'
+            numpy: '1.20.*'
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        id: python
+        with:
+          python-version: ${{ matrix.python }}
+      - uses: actions/cache@v3
+        with:
+          path: ${{ env.pythonLocation }}
+          key: test-numpy${{ matrix.numpy }}-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml', '**/setup.*') }}
+      - run: pip install -e ".[test]" pytest-xdist
+      - run: pip install numpy==${{ matrix.numpy }}
+      - run: pip freeze
+      - run: pytest -n auto
+  test_with_coverage:
+    name: test with coverage
+    needs: [ test, test_alldeps, test_devdeps, test_pyargs, test_older_numpy ]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        id: python
+        with:
+          python-version: 3.9
+      - uses: actions/cache@v3
+        with:
+          path: ${{ env.pythonLocation }}
+          key: test-coverage-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml', '**/setup.*') }}
+      - run: pip install ".[test]" pytest-xdist pytest-cov
+      - run: pip freeze
+      - run: pytest -n auto --cov-report xml --cov-report term-missing --cov .
+      - uses: codecov/codecov-action@v3
+        with:
+          file: ./coverage.xml
+          flags: unit
+          fail_ci_if_error: true
+  build_docs:
+    name: build HTML docs
+    needs: [ test, test_alldeps, test_devdeps, test_pyargs, test_older_numpy ]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        id: python
+        with:
+          python-version: 3.9
+      - uses: actions/cache@v3
+        with:
+          path: ${{ env.pythonLocation }}
+          key: build-docs-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml', '**/setup.*') }}
+      - run: sudo apt-get install graphviz texlive-latex-extra dvipng
+      - run: pip install ".[docs]"
+      - run: pip freeze
+      - run: sphinx-build -W docs docs/_build

pytest.ini

@@ -0,0 +1,4 @@
+[pytest]
+markers =
+	soctests: run only the SOC tests in the suite.
+

regtest/test_l1.py

@@ -0,0 +1,16 @@
+"""
+Regression tests for Level 1 generation.
+"""
+
+import pytest
+
+
+@pytest.mark.bigdata
+def test_dummy_reg():
+    assert 1 > 0
+
+
+@pytest.mark.bigdata
+@pytest.mark.soctests
+def test_dummy_soctest_reg():
+    assert 1 > 0

romanisim/apt.py

@@ -6,8 +6,7 @@
 fraction of what an APT file seems able to do.
 """
 
-import xml
-from xml.etree import ElementTree
+import defusedxml.ElementTree
 from astropy import coordinates
 from astropy import units as u
 import dataclasses
@@ -48,7 +47,8 @@ def read_apt(filename):
     """
     # I don't know anything about reading XML.
     # In general it's very flexible and can do anything.
-    tree = ElementTree.parse(filename)
+    # tree = ElementTree.parse(filename)
+    tree = defusedxml.ElementTree.parse(filename)
     targs = tree.find(XMLNS + 'Targets')
     target_elements = targs.findall(XMLNS + 'FixedTarget')
     target_dict = dict()

romanisim/bandpass.py

@@ -24,7 +24,7 @@
 # the galsim bandpass names to the Roman bandpass names and vice versa.
 # it would be nice to be agnostic about which one we use.
 galsim_bandpasses = ['Z087', 'Y106', 'J129', 'H158', 'F184', 'W149']
-galsim2roman_bandpass = {x: 'F'+x[1:] for x in galsim_bandpasses}
+galsim2roman_bandpass = {x: 'F' + x[1:] for x in galsim_bandpasses}
 roman2galsim_bandpass = {v: k for k, v in galsim2roman_bandpass.items()}
 
 # provide some no-ops if we are given a key in the right bandpass
@@ -84,13 +84,13 @@ def compute_abflux(effarea=None):
     out = dict()
     for bandpass in filter_names:
         integrand = abfv * constants.c / (
-            effarea['Wave']*u.micron)**2  # f_lambda
+            effarea['Wave'] * u.micron)**2  # f_lambda
         integrand /= constants.h * constants.c / (
-            effarea['Wave']*u.micron)  # hc/lambda
-        integrand *= effarea[bandpass]*u.m**2  # effective area in filter
+            effarea['Wave'] * u.micron)  # hc/lambda
+        integrand *= effarea[bandpass] * u.m**2  # effective area in filter
         # integrate.simpson looks like it loses units.  So convert to something
         # we know about.
-        integrand = integrand.to(1/(u.s*u.micron)).value
+        integrand = integrand.to(1 / (u.s * u.micron)).value
         zpflux = integrate.simpson(integrand, effarea['Wave'])
         # effarea['Wave'] is in microns, so we're left with a number of counts
         # per second

romanisim/catalog.py

@@ -75,8 +75,8 @@ def make_dummy_catalog(coord, radius=0.1, rng=None, seed=42, nobj=1000,
         elif p < 0.9:  # 10% of targets; stars
             mu_x = 1.e5
             sigma_x = 2.e5
-            mu = np.log(mu_x**2 / (mu_x**2+sigma_x**2)**0.5)
-            sigma = (np.log(1 + sigma_x**2/mu_x**2))**0.5
+            mu = np.log(mu_x**2 / (mu_x**2 + sigma_x**2)**0.5)
+            sigma = (np.log(1 + sigma_x**2 / mu_x**2))**0.5
             gd = galsim.GaussianDeviate(rng, mean=mu, sigma=sigma)
             flux = np.exp(gd()) / roman.exptime
             if chromatic:
@@ -132,7 +132,7 @@ def make_dummy_table_catalog(coord, radius=0.1, rng=None, nobj=1000,
     # at least not crazy for a dummy catalog
     faintmag = 26 - 3  # get some brighter sources!
     hlr_at_faintmag = 0.6  # arcsec
-    mag = faintmag - np.random.exponential(size=nobj, scale=5/3/np.log(10))
+    mag = faintmag - np.random.exponential(size=nobj, scale=5 / 3 / np.log(10))
     # okay, now we need to mark some star/galaxy decisions.
     sersic_index = np.random.uniform(low=1, high=4.0, size=nobj)
     star = np.random.uniform(size=nobj) < 0.1
@@ -148,10 +148,10 @@ def make_dummy_table_catalog(coord, radius=0.1, rng=None, nobj=1000,
     ba = np.clip(ba, 0.2, 1)
     ba[star] = 1
     # ugh.  Half light radii should correlate with magnitude, with some scatter.
-    hlr = 10**((faintmag - mag)/5) * hlr_at_faintmag
+    hlr = 10**((faintmag - mag) / 5) * hlr_at_faintmag
     # hlr is hlr_at_faintmag for faintmag sources
     # and let's put some log normal distribution on top of this
-    hlr *= np.clip(np.exp(np.random.randn(nobj)*0.5), 0.1, 10)
+    hlr *= np.clip(np.exp(np.random.randn(nobj) * 0.5), 0.1, 10)
     # let's not make anything too too small.
     hlr[hlr < 0.01] = 0.01
     hlr[star] = 0
@@ -168,7 +168,7 @@ def make_dummy_table_catalog(coord, radius=0.1, rng=None, nobj=1000,
         mag_thisband = mag + np.random.randn(nobj)
         # sigma of one mag isn't nuts.  But this will be totally uncorrelated
         # in different bands, so we'll get some weird colored objects
-        out[bandpass] = 10.**(-mag_thisband/2.5)
+        out[bandpass] = 10.**(-mag_thisband / 2.5)
         # maggies!  what units should I actually pick here?
     return out
 
@@ -209,7 +209,7 @@ def table_to_catalog(table, bandpasses):
 
     out = list()
     for i in range(len(table)):
-        pos = coordinates.SkyCoord(table['ra'][i]*u.deg, table['dec'][i]*u.deg,
+        pos = coordinates.SkyCoord(table['ra'][i] * u.deg, table['dec'][i] * u.deg,
                                    frame='icrs')
         pos = util.celestialcoord(pos)
         fluxes = {bp: table[bp][i] for bp in bandpasses}
@@ -218,7 +218,7 @@ def table_to_catalog(table, bandpasses):
         elif table['type'][i] == 'SER':
             obj = galsim.Sersic(table['n'][i], table['half_light_radius'][i])
             obj = obj.shear(
-                q=table['ba'][i], beta=(table['pa'][i]+np.pi/2)*galsim.radians)
+                q=table['ba'][i], beta=(table['pa'][i] + np.pi / 2) * galsim.radians)
         else:
             raise ValueError('Catalog types must be either PSF or SER.')
         out.append(CatalogObject(pos, obj, fluxes))