Created pipeline-specific environment file

environment_pipeline.sh

@@ -0,0 +1,29 @@
+export env_name="jwql-pipeline"
+export PIPELINE_VERSION=$(<environment_pipeline_version.txt)
+
+case `uname` in
+    Darwin)
+        if ! command -v conda &> /dev/null
+        then
+            curl https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -o installer.sh
+            ./installer.sh -b -p ./miniconda3_tmp
+            conda init zsh
+        fi
+        conda create -n ${env_name} --file https://ssb.stsci.edu/releases/jwstdp/${PIPELINE_VERSION}/conda_python_macos-stable-deps.txt
+        conda activate ${env_name}
+        pip install -r https://ssb.stsci.edu/releases/jwstdp/${PIPELINE_VERSION}/reqs_macos-stable-deps.txt
+    ;;
+    Linux)
+        if ! command -v conda &> /dev/null
+        then
+            curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o installer.sh
+            ./installer.sh -b -p ./miniconda3_tmp
+            conda init zsh
+        fi
+        conda create -n ${env_name} --file https://ssb.stsci.edu/releases/jwstdp/${PIPELINE_VERSION}/conda_python_stable-deps.txt
+        conda activate ${env_name}
+        pip install -r https://ssb.stsci.edu/releases/jwstdp/${PIPELINE_VERSION}/reqs_stable-deps.txt
+    ;;
+esac
+
+conda env update --name ${env_name} --file environment_pipeline.yml --prune

environment_pipeline.yml

@@ -0,0 +1,61 @@
+# This file describes a conda environment that can be used to install the jwql
+# pipeline processing environment. It is not a standalone environment, but instead is 
+# intended as a supplement to the JWST pipeline environments stored online at STScI.
+#
+# Run the following command to set up this environment:
+# $ source environment_pipeline.sh
+#
+# Note that this environment takes the pipeline version from the file
+# 
+#   environment_pipeline_version.txt
+#
+# Run the following command to activate the environment:
+# $ source activate jwql-pipeline
+#
+# To deactivate the environment run the following command:
+# $ source deactivate
+#
+# To remove the environment entirely, run the following command:
+# $ conda env remove -n jwql-pipeline
+
+name: jwql-pipeline
+
+channels:
+  - defaults
+
+dependencies:
+  - bokeh=2.4.2
+  - beautifulsoup4=4.11.1
+  - celery
+  - cryptography=36.0.0
+  - django=3.2.5
+  - inflection=0.5.1
+  - ipython=8.2.0
+  - jinja2=3.0.2
+  - nodejs=10.13.0
+  - numpydoc
+  - pandas=1.4.2
+  - pip=21.0.1
+  - postgresql=12.2
+  - psycopg2=2.8.6
+  - redis
+  - setuptools=52.0.0
+  - sphinx=4.2.0
+  - sphinx_rtd_theme=0.4.3
+  - sqlalchemy=1.4.32
+  - twine=3.7.1
+  - wtforms=2.3.3
+
+  - pip:
+    - astroquery==0.4.6
+    - bandit==1.7.4
+    - pysiaf==0.15.0
+    - pysqlite3==0.4.7
+    - pyvo==1.3
+    - stsci_rtd_theme==0.0.2
+    - git+https://github.com/spacetelescope/jwst_reffiles
+    - vine==1.3.0
+    - redis
+
+    # Current package
+    - -e .

environment_pipeline_version.txt

@@ -0,0 +1 @@
+1.4.6

jwql/instrument_monitors/common_monitors/bad_pixel_monitor.py

@@ -790,8 +790,11 @@ def process(self, illuminated_raw_files, illuminated_slope_files, dark_raw_files
                     short_name = os.path.basename(uncal_file).replace('_uncal.fits', '')
                     local_uncal_file = os.path.join(self.data_dir, os.path.basename(uncal_file))
                     logging.info('Calling pipeline for {}'.format(uncal_file))
-                    logging.info("Copying raw file to {}".format(self.data_dir))
-                    copy_files([uncal_file], self.data_dir)
+                    if os.path.isfile(local_uncal_file):
+                        logging.info("Local uncalibrated file exists")
+                    else:
+                        logging.info("Copying raw file to {}".format(self.data_dir))
+                        copy_files([uncal_file], self.data_dir)
                     if hasattr(self, 'nints') and self.nints > 1:
                         out_exts[short_name] = ['jump', '1_ramp_fit']
                     in_files.append(local_uncal_file)
@@ -828,9 +831,12 @@ def process(self, illuminated_raw_files, illuminated_slope_files, dark_raw_files
             out_exts = defaultdict(lambda: ['jump', 'fitopt', '0_ramp_fit'])
             for uncal_file, rate_file in zip(dark_raw_files, dark_slope_files):
                 logging.info('Calling pipeline for {} {}'.format(uncal_file, rate_file))
-                logging.info("Copying raw file to {}".format(self.data_dir))
-                copy_files([uncal_file], self.data_dir)
                 local_uncal_file = os.path.join(self.data_dir, os.path.basename(uncal_file))
+                if os.path.isfile(local_uncal_file):
+                    logging.info("Local uncalibrated file exists")
+                else:
+                    logging.info("Copying raw file to {}".format(self.data_dir))
+                    copy_files([uncal_file], self.data_dir)
                 short_name = os.path.basename(uncal_file).replace('_uncal.fits', '')
                 if hasattr(self, 'nints') and self.nints > 1:
                     out_exts[short_name] = ['jump', 'fitopt', '1_ramp_fit']