Merge pull request #32 from oirlab/update_jwst_0.17.0

Update jwst 0.17.0 and CRDS 7.5.0.2

.github/workflows/python-package.yml

@@ -40,19 +40,19 @@ jobs:
       env:
           C_INCLUDE_PATH: /usr/include/cfitsio/
     - name: Test
-      run: |  
-        source setup_local_crds.sh && python setup.py test
+      run: |
+        source setup_local_crds.sh && pytest
     - name: Build docs
       if: ${{ matrix.python-version==3.6 }}
-      run: |  
+      run: |
         python -m pip install -r docs/requirements.txt && sphinx-multiversion docs html
     - name: Install SSH Client 🔑
       if: ${{ matrix.python-version==3.6 }}
       uses: webfactory/[email protected]
       with:
         ssh-private-key: ${{ secrets.DEPLOY_KEY }}
     - name: Deploy 🚀
-      if: ${{ matrix.python-version==3.6 && contains(github.ref, 'master') }}  
+      if: ${{ matrix.python-version==3.6 && contains(github.ref, 'master') }}
       uses: JamesIves/[email protected]
       with:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

iris_pipeline/pipeline/image2.py

@@ -60,6 +60,11 @@ def process(self, input):
             self.log.info("Processing product {}".format(product["name"]))
             if self.save_results:
                 self.output_file = product["name"]
+            try:
+                getattr(asn, 'filename')
+            except AttributeError:
+                asn.filename = "singleton"
+
             result = self.process_exposure_product(
                 product, asn["asn_pool"], op.basename(asn.filename)
             )

iris_pipeline/pipeline/preprocess_flatfield.py

@@ -42,6 +42,10 @@ def process(self, input):
             self.log.info("Processing product {}".format(product["name"]))
             if self.save_results:
                 self.output_file = product["name"]
+            try:
+                getattr(asn, 'filename')
+            except AttributeError:
+                asn.filename = "singleton"
             result = self.process_exposure_product(
                 product, asn["asn_pool"], op.basename(asn.filename)
             )

iris_pipeline/tests/test_image2.py

@@ -44,9 +44,9 @@ def test_image2_subarray(tmp_path):
     input_model.meta.subarray.ysize = ysize
     subarray_slice = np.s_[ystart:ystart+ysize, xstart:xstart+xsize]
 
-    input_model.data = input_model.data[subarray_slice]
-    input_model.dq = input_model.dq[subarray_slice]
-    input_model.err = input_model.err[subarray_slice]
+    input_model.data = np.array(input_model.data[subarray_slice])
+    input_model.dq = np.array(input_model.dq[subarray_slice])
+    input_model.err = np.array(input_model.err[subarray_slice])
 
     raw_science_subarray_filename = tmp_path / "temp_subarray_science.fits"
     input_model.write(raw_science_subarray_filename)

iris_pipeline/tests/test_utils.py

@@ -21,4 +21,7 @@ def get_data_from_url(filename):
     ):
         warnings.warn(f"Retrieve data for {filename} (if not cached already)")
         local_path = data.get_pkg_data_filename(filename, show_progress=True)
-    return local_path
+        local_path_suffix = local_path + ".fits"
+        if not os.path.exists(local_path_suffix):
+            os.symlink(local_path, local_path_suffix)
+    return local_path_suffix

pytest.ini

@@ -3,5 +3,6 @@ log_cli = 0
 log_cli_level = INFO
 log_cli_format = %(asctime)s [%(levelname)8s] %(message)s (%(filename)s:%(lineno)s)
 log_cli_date_format=%Y-%m-%d %H:%M:%S
+addopts = --nbval-lax --current-env
 testpaths =
     iris_pipeline/tests

requirements.txt

@@ -1,3 +1,3 @@
 astropy
 git+https://github.com/oirlab/tmt-crds.git
-https://github.com/spacetelescope/jwst/archive/0.13.7.zip
+git+https://github.com/spacetelescope/jwst@0.17.0