HLA-1145: New drizzlepac release candidate 3.6.2rc1 (#1685)

Co-authored-by: Nadia Dencheva <[email protected]> Co-authored-by: Steve Goldman <[email protected]> Co-authored-by: Zach Burnett <[email protected]> Co-authored-by: Zach Burnett <[email protected]>
spacetelescope · Oct 27, 2023 · 438c4dd · 438c4dd
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diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -0,0 +1,18 @@
+<!-- If this PR closes a JIRA ticket, make sure the title starts with the JIRA issue number,
+for example HLA-1234: <Fix a bug> -->
+Resolves [HLA-nnnn](https://jira.stsci.edu/browse/HLA-nnnn)
+
+<!-- If this PR closes a GitHub issue, reference it here by its number -->
+Closes #
+
+<!-- describe the changes comprising this PR here -->
+This PR addresses ...
+
+**Checklist for maintainers**
+- [ ] added entry in `CHANGELOG.rst` within the relevant release section
+- [ ] updated or added relevant tests
+- [ ] updated relevant documentation
+- [ ] added relevant milestone
+- [ ] added relevant label(s)
+- [ ] ran regression tests, post a link to the Jenkins job below.
+      [How to run regression tests on a PR](https://github.com/spacetelescope/jwst/wiki/Running-Regression-Tests-Against-PR-Branches)
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -0,0 +1,23 @@
+name: build
+
+on:
+  release:
+    types: [ released ]
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  build:
+    uses: OpenAstronomy/github-actions-workflows/.github/workflows/publish.yml@v1
+    with:
+      upload_to_pypi: ${{ (github.event_name == 'release') && (github.event.action == 'released') }}
+      targets: |
+        # Linux wheels
+        - cp3*-manylinux_x86_64
+        # MacOS wheels
+        - cp3*-macosx_x86_64
+        # Until we have arm64 runners, we can't automatically test arm64 wheels
+#        - cp3*-macosx_arm64
+      sdist: true
+    secrets:
+      pypi_token: ${{ secrets.PYPI_PASSWORD_STSCI_MAINTAINER }}
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -42,7 +42,6 @@ jobs:
     with:
       envs: |
         - linux: check-style
-        - linux: check-build
   test:
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1
     needs: [ crds ]

diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -25,9 +25,8 @@ conda:
   environment: doc/.rtd-environment.yml
 
 python:
-  system_packages: false
   install:
     - method: pip
       path: .
       extra_requirements:
-        - docs
+        - docs
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -21,6 +21,10 @@ number of the code change for that issue.  These PRs can be viewed at:
 3.6.2rc0 (unreleased)
 =====================
 
+- Added functionality to allow the use of a two-column poller file. This is used
+  to update the WFPC2 SVM aperture header keywords from the values in the poller 
+  file.
+
 - Removed the version restriction on matplotlib. [#1649]
 
 - Forced a preferential order on the final selection of the WCS solution 

diff --git a/JenkinsfileRT b/JenkinsfileRT
@@ -22,10 +22,10 @@ bc1.nodetype = 'linux'
 bc1.env_vars = ['TEST_BIGDATA=https://bytesalad.stsci.edu/artifactory']
 bc1.name = '3.9'
 bc1.conda_packages = ['python=3.9']
-bc1.build_cmds = ["pip install numpy astropy codecov pytest-cov ci-watson==0.5",
+bc1.build_cmds = ["pip install numpy astropy codecov pytest-cov ci-watson",
 		 "pip install --upgrade -e '.[test]'",
                  "pip freeze"]
-bc1.test_cmds = ["pytest --cov=./ --basetemp=tests_output --junitxml results.xml --bigdata",
+bc1.test_cmds = ["pytest --cov=./ --basetemp=tests_output --junitxml=results.xml --bigdata",
                 "codecov"]
 bc1.test_configs = [data_config]
 bc1.failedFailureThresh = 0
@@ -38,20 +38,18 @@ bc3 = new BuildConfig()
 bc3.runtime.add('CFLAGS=-std=gnu99')
 bc3.nodetype = 'linux'
 bc3.env_vars = ['TEST_BIGDATA=https://bytesalad.stsci.edu/artifactory']
-bc3.name = '3.10-dev'
+bc3.name = '3.10'
 bc3.conda_packages = ['python=3.10']
-bc3.build_cmds = ["pip install numpy astropy codecov pytest-cov ci-watson==0.5",
-		 "pip install -r requirements-dev.txt --upgrade -e '.[test]'",
+bc3.build_cmds = ["pip install numpy astropy ci-watson",
+		 "pip install --upgrade -e '.[test]'",
                  "pip freeze"]
-bc3.test_cmds = ["pytest --cov=./ --basetemp=tests_output --bigdata",
-                "codecov"]
 bc3.test_configs = [data_config]
 
 bc4 = utils.copy(bc3)
-bc4.name = '3.11-dev'
+bc4.name = '3.11'
 bc4.conda_packages = ['python=3.11']
 
 // Iterate over configurations that define the (distributed) build matrix.
 // Spawn a host (or workdir) for each combination and run in parallel.
 // Also apply the job configuration defined in `jobconfig` above.
-utils.run([bc1, bc3, bc4, jobconfig])
+utils.run([bc1, bc2, bc3, bc4, jobconfig])
diff --git a/README.md b/README.md
@@ -1,7 +1,6 @@
 # Drizzlepac
 
-[![Build Status](https://dev.azure.com/spacetelescope/drizzlepac/_apis/build/status/spacetelescope.drizzlepac?branchName=master)](https://dev.azure.com/spacetelescope/drizzlepac/_build/latest?definitionId=2&branchName=master)
-[![Build Status](https://ssbjenkins.stsci.edu/job/STScI/job/drizzlepac/job/master/badge/icon)](https://ssbjenkins.stsci.edu/job/STScI/job/drizzlepac/job/master/)
+[![Build Status](https://github.com/spacetelescope/drizzlepac/actions/workflows/ci.yml/badge.svg)](https://github.com/spacetelescope/drizzlepac/actions/workflows/ci.yml)
 [![Documentation Status](https://readthedocs.org/projects/drizzlepac/badge/?version=latest)](http://drizzlepac.readthedocs.io/en/latest/?badge=latest)
 [![codecov](https://codecov.io/gh/spacetelescope/drizzlepac/branch/master/graph/badge.svg)](https://codecov.io/gh/spacetelescope/drizzlepac)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3743274.svg)](https://doi.org/10.5281/zenodo.3743274)
@@ -23,10 +22,7 @@ can be found at:
 
 ## Conda (Recommended)
 
-```bash
-$ conda config --add channels http://ssb.stsci.edu/astroconda
-$ conda create -n astroconda stsci
-```
+`Drizzlepac` is installed when you install the `stenv` conda environment (a replacement for `astroconda`). Select your desired release and follow the instructions on the [`stenv` installation page](https://stenv.readthedocs.io/en/latest/getting_started.html). 
 
 ## From Source
 

diff --git a/doc/source/getting_started/installation.rst b/doc/source/getting_started/installation.rst
@@ -1,4 +1,47 @@
 Installation
 ------------
 
-*Coming soon!*
+Conda (Recommended)
+===================
+
+``Drizzlepac`` is installed when you install the ``stenv`` conda environment (a replacement for ``astroconda``). Select your desired release and follow the instructions on the `installation page <https://stenv.readthedocs.io/en/latest/getting_started.html>`_. 
+
+
+From Source
+===========
+
+Clone this repository
+*********************
+.. code-block:: shell
+
+    git clone https://github.com/spacetelescope/drizzlepac
+    cd drizzlepac
+
+
+Build the documentation
+=======================
+
+*Note:* If you intend to use ``drizzlepac``'s embedded help feature from within
+an interactive ``python`` or ``ipython`` session, we recommend you do not skip
+this step.
+
+
+.. code-block:: shell
+
+    cd doc/
+    make html
+
+
+Install drizzlepac
+==================
+
+.. code-block:: shell
+
+    pip install .
+
+The option ``--no-use-pep517`` MAY be required in order to correctly build 
+the C extensions with ``pip`` versions up to 22.2, after commenting out 
+the ``build-backend`` from the ``pyproject.toml`` config file.
+
+**Support for installing using `pip` is still evolving, so use of this 
+command is provided on an experimental basis for now.**
diff --git a/drizzlepac/align.py b/drizzlepac/align.py
@@ -367,7 +367,7 @@ def perform_align(
     hdr0 = fits.getheader(imglist[0])
     inst = hdr0.get("instrume")
     if inst.lower() == "wfpc2" and "detector" not in hdr0:
-        det = "wfpc2"
+        det = "pc"
     else:
         det = hdr0.get("detector")
     apars = get_default_pars(inst, det)
@@ -961,7 +961,7 @@ def determine_fit_quality(
             if catalogs_remaining:
                 log.warning(
                     "Not enough cross matches found between astrometric"
-                    " catalog and sources found in {}".format(image_name)
+                    " catalog and sources found in {} ()".format(image_name, num_xmatches)
                 )
                 continue
 
@@ -1158,7 +1158,7 @@ def determine_fit_quality(
     if not overall_valid:
         log.info("The fit solution for some or all of the images is not valid.")
     if max_rms_val > auto_good_rms or not overall_valid:
-        log.info("Try again with the next catalog")
+        log.info("Trying again with the next catalog, method, or geometry depending upon the current fitting cycle.")
     else:
         log.info("Fit calculations successful.")
 

diff --git a/drizzlepac/hapsequencer.py b/drizzlepac/hapsequencer.py
@@ -94,7 +94,7 @@
                   "SVM_CATALOG_WFC": 'on',
                   "SVM_CATALOG_UVIS": 'on',
                   "SVM_CATALOG_IR": 'on',
-                  "SVM_CATALOG_WFPC2": 'on'}
+                  "SVM_CATALOG_PC": 'on'}
 envvar_cat_str = "SVM_CATALOG_{}"
 
 # --------------------------------------------------------------------------------------------------------------
@@ -122,7 +122,7 @@ def create_catalog_products(total_obj_list, log_level, diagnostic_mode=False, ph
                        Specify which, if any, catalogs should be generated at all, based on detector.  This dictionary
                        needs to contain values for all instruments; namely:
 
-                       SVM_CATALOG_HRC, SVM_CATALOG_SBC, SVM_CATALOG_WFC, SVM_CATALOG_UVIS, SVM_CATALOG_IR, SVM_CATALOG_WFPC2
+                       SVM_CATALOG_HRC, SVM_CATALOG_SBC, SVM_CATALOG_WFC, SVM_CATALOG_UVIS, SVM_CATALOG_IR, SVM_CATALOG_PC
 
                        These variables can be defined with values of 'on'/'off'/'yes'/'no'/'true'/'false'.
 
@@ -765,10 +765,10 @@ def run_align_to_gaia(tot_obj, log_level=logutil.logging.INFO, diagnostic_mode=F
     for exp_obj in tot_obj.edp_list:
         if gaia_obj is None:
             prod_list = exp_obj.info.split("_")
-            prod_list[4] = "metawcs"
+            prod_list[5] = "metawcs"
             gaia_obj = product.FilterProduct(prod_list[0], prod_list[1], prod_list[2],
-                                             prod_list[3], prod_list[4], "all",
-                                             prod_list[5][0:3], log_level)
+                                             prod_list[3], prod_list[4], prod_list[5], "all",
+                                             prod_list[6][0:3], log_level)
             gaia_obj.configobj_pars = tot_obj.configobj_pars
         gaia_obj.add_member(exp_obj)
 

diff --git a/drizzlepac/haputils/align_utils.py b/drizzlepac/haputils/align_utils.py
@@ -174,7 +174,7 @@ def __init__(self, input_list, clobber=False, dqname='DQ', process_type='',
                 hdr0 = fits.getheader(img)
                 instrume = hdr0.get('instrume')
                 if instrume.lower() == 'wfpc2' and 'detector' not in hdr0:
-                    detector = 'WFPC2'
+                    detector = 'PC'
                 else:
                     detector = hdr0.get('detector')
 

diff --git a/drizzlepac/haputils/astrometric_utils.py b/drizzlepac/haputils/astrometric_utils.py
@@ -167,6 +167,7 @@
                'mag': 'mag', 'objID': 'objID', 'epoch': 'epoch'},
     }
 
+log.info(f'ASTROMETRIC_CATALOG_URL = {SERVICELOCATION}')
 
 # CRBIT definitions
 CRBIT = 4096
@@ -181,7 +182,7 @@ def create_astrometric_catalog(inputs, catalog="GAIAedr3", output="ref_cat.ecsv"
                                gaia_only=False, table_format="ascii.ecsv",
                                existing_wcs=None, num_sources=None,
                                use_footprint=False, full_catalog=False,
-                               user_epoch='match', log_level=logutil.logging.NOTSET):
+                               user_epoch='match', log_level=logutil.logging.INFO):
     """Create an astrometric catalog that covers the inputs' field-of-view.
 
     This function will return a table containing sources derived from the
@@ -451,7 +452,7 @@ def get_catalog(ra, dec, sr=0.1, epoch=None, catalog='GSC241'):
     spec = base_spec + epoch_str.format(epoch) if epoch else base_spec
 
     serviceUrl = '{}/{}?{}'.format(SERVICELOCATION, serviceType, spec)
-    log.debug("Getting catalog using: \n    {}".format(serviceUrl))
+    log.info(f"Getting catalog using: \n    {serviceUrl}")
     rawcat = requests.get(serviceUrl, headers=headers)
     r_contents = rawcat.content.decode()  # convert from bytes to a String
     rstr = r_contents.split('\r\n')
@@ -460,7 +461,7 @@ def get_catalog(ra, dec, sr=0.1, epoch=None, catalog='GSC241'):
     if rstr[0].startswith('Error'):
         # Try again without EPOCH
         serviceUrl = '{}/{}?{}'.format(SERVICELOCATION, serviceType, base_spec)
-        log.debug("Getting catalog using: \n    {}".format(serviceUrl))
+        log.warning(f"Problem accessing catalog service - getting catalog using: \n    {serviceUrl}")
         rawcat = requests.get(serviceUrl, headers=headers)
         r_contents = rawcat.content.decode()  # convert from bytes to a String
         rstr = r_contents.split('\r\n')
@@ -522,7 +523,7 @@ def get_catalog_from_footprint(footprint, epoch=None, catalog='GSC241'):
     spec = base_spec + epoch_str.format(epoch) if epoch else base_spec
 
     serviceUrl = '{}/{}?{}'.format(SERVICELOCATION, serviceType, spec)
-    log.debug("Getting catalog using: \n    {}".format(serviceUrl))
+    log.info(f"Getting catalog from footprint using: \n    {serviceUrl}")
 
     rawcat = requests.get(serviceUrl, headers=headers)
     r_contents = rawcat.content.decode()  # convert from bytes to a String
@@ -532,7 +533,7 @@ def get_catalog_from_footprint(footprint, epoch=None, catalog='GSC241'):
     if rstr[0].startswith('Error'):
         # Try again without EPOCH
         serviceUrl = '{}/{}?{}'.format(SERVICELOCATION, serviceType, base_spec)
-        log.debug("Getting catalog using: \n    {}".format(serviceUrl))
+        log.warning(f"Problem accessing catalog service - getting catalog from footprint using: \n    {serviceUrl}")
         rawcat = requests.get(serviceUrl, headers=headers)
         r_contents = rawcat.content.decode()  # convert from bytes to a String
         rstr = r_contents.split('\r\n')
@@ -719,7 +720,7 @@ def compute_2d_background(imgarr, box_size, win_size,
 
 def build_auto_kernel(imgarr, whtarr, fwhm=3.0, threshold=None, source_box=7,
                       good_fwhm=[1.0, 4.0], num_fwhm=30,
-                      isolation_size=11, saturation_limit=70000., log_level=logutil.logging.NOTSET):
+                      isolation_size=11, saturation_limit=70000., log_level=logutil.logging.INFO):
     """Build kernel for use in source detection based on image PSF
     This algorithm looks for an isolated point-source that is non-saturated to use as a template
     for the source detection kernel.  Failing to find any suitable sources, it will return a
@@ -898,7 +899,7 @@ def find_fwhm(psf, default_fwhm):
 
 def extract_point_sources(img, dqmask=None, fwhm=3.0, kernel=None,
                           nbright=1000,
-                          threshold=200.0, sigma=3.0, source_box=7, log_level=logutil.logging.NOTSET):
+                          threshold=200.0, sigma=3.0, source_box=7, log_level=logutil.logging.INFO):
     """Use photutils to replicate the IRAF point-source catalogs"""
     # Initialize logging for this user-callable function
     log.setLevel(log_level)
@@ -961,7 +962,7 @@ def extract_sources(img, dqmask=None, fwhm=3.0, kernel=None, photmode=None,
                     dao_nsigma=3.0, source_box=7,
                     classify=True, centering_mode="starfind", nlargest=None,
                     outroot=None, plot=False, vmax=None, deblend=False,
-                    log_level=logutil.logging.NOTSET):
+                    log_level=logutil.logging.INFO):
     """Use photutils to find sources in image based on segmentation.
 
     Parameters