Merge pull request #373 from simontorres/small_fixes_2023

Small fixes 2023

.github/workflows/python-package.yml

@@ -18,9 +18,9 @@ jobs:
         python-version: ['3.8', '3.9', '3.10', '3.11']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
@@ -30,10 +30,10 @@ jobs:
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Compile DCR Binaries
       run: |
-        SOURCE_DIR=${{ github.workspace }}/goodman_pipeline/data/dcr-source/dcr
+        SOURCE_DIR=${{ github.workspace }}/goodman_pipeline/data/dcr_source/dcr
         make --directory $SOURCE_DIR
         chmod +x $SOURCE_DIR/dcr
-        echo "${{ github.workspace }}/goodman_pipeline/data/dcr-source/dcr" >> $GITHUB_PATH
+        echo "${{ github.workspace }}/goodman_pipeline/data/dcr_source/dcr" >> $GITHUB_PATH
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
@@ -44,7 +44,7 @@ jobs:
       run: |
         pytest --cov=goodman_pipeline
 
-    - uses: codecov/codecov-action@v1
+    - uses: codecov/codecov-action@v3
       with:
         token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
         fail_ci_if_error: true # optional (default = false)

.gitignore

@@ -7,8 +7,8 @@ __pycache__/*
 .ipynb_checkpoints/*
 files.txt
 docs/_build/*
-goodman_pipeline/data/dcr-source/dcr
-goodman_pipeline/data/dcr-source/*.o
+goodman_pipeline/data/dcr_source/dcr
+goodman_pipeline/data/dcr_source/*.o
 /dev-tools/
 .cache/*
 .eggs/*

docs/_file_suffixes.rst

@@ -25,4 +25,33 @@ There are two scenarios where this can happen:
     ================ ========= ========================================
 
 
-Assuming the two targets in `sci_file.fits` are extracted we'll end up with
+Assuming the two targets in `sci_file.fits` are extracted and they are approximately at the position
+400 and 600 (pixels in spatial axis), after extraction we'll end up with:
+
+.. code-block:: bash
+
+  esci_file_target_1.fits
+  esci_file_target_2.fits
+  elamp_001_390-410.fits
+  elamp_001_590-610.fits
+  elamp_002_390-410.fits
+  elamp_002_590-610.fits
+
+
+The default prefix for extraction is ``e`` and does not have an underscore to separate it from the
+file name.
+
+After wavelength calibration, since there are two suitable lamps and due to the fact that the
+pipeline does not combine solutions, it will save two wavelength calibrated files with each one
+solved by the respective lamp. Then:
+
+.. code-block:: bash
+
+  wesci_file_target_1_ws_1.fits
+  wesci_file_target_1_ws_2.fits
+  wesci_file_target_2_ws_1.fits
+  wesci_file_target_2_ws_2.fits
+  welamp_001_390-410.fits
+  welamp_001_590-610.fits
+  welamp_002_390-410.fits
+  welamp_002_590-610.fits

docs/_install_dcr.rst

@@ -16,7 +16,7 @@ of LACosmic.
 The latest version of the Goodman Spectroscopic Pipeline uses a modified version
 of ``dcr`` to help with the pipeline's workflow. It is included under
 
-  ``<path_to_download_location>/goodman_pipeline/goodman_pipeline/data/dcr-source/dcr/``
+  ``<path_to_download_location>/goodman_pipeline/goodman_pipeline/data/dcr_source/dcr/``
 
 ``goodman_pipeline-<version>`` is the folder that will be created once you untar or unzip the latest
 release of the |pipeline name|.
@@ -38,7 +38,7 @@ Compiling DCR
 
 Compiling ``dcr`` is actually very simple.
 
-  ``cd <path_to_download_location>/goodman_pipeline/goodman_pipeline/data/dcr-source/dcr/``
+  ``cd <path_to_download_location>/goodman_pipeline/goodman_pipeline/data/dcr_source/dcr/``
 
 Then simply type:
 

docs/conf.py

@@ -39,7 +39,7 @@
               'sphinx.ext.autodoc',
               'sphinx.ext.mathjax',
               'sphinx.ext.intersphinx',
-              'sphinxcontrib.napoleon']
+              'sphinx.ext.napoleon']
 
 
 intersphinx_mapping = {
@@ -81,7 +81,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

environment.yml

@@ -6,13 +6,13 @@ dependencies:
   - matplotlib
   - scipy
   - cython
-  - astropy
   - pip
   - pip:
-    - ccdproc
-    - coveralls
-    - pydata-sphinx-theme
-    - astroplan
-    - mock
-    - sphinx
-    - sphinxcontrib.napoleon
+      - astropy>=5.3
+      - ccdproc
+      - coveralls
+      - pydata-sphinx-theme
+      - astroplan
+      - mock
+      - sphinx
+      - sphinxcontrib.napoleon

goodman_pipeline/core/core.py

@@ -1149,7 +1149,7 @@ def extraction(ccd,
 
 def extract_fractional_pixel(ccd, target_trace, target_fwhm, extraction_width,
                              background_spacing=3):
-    """Performs an spectrum extraction using fractional pixels.
+    """Performs a spectrum extraction using fractional pixels.
 
     Args:
         ccd (CCDData) Instance of :class:`~astropy.nddata.CCDData` that

goodman_pipeline/version.py

@@ -1,2 +1,2 @@
 # This is an automatic generated file please do not edit
-__version__ = '1.3.6'
+__version__ = '1.3.7'

install_dcr.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-SOURCE_DIR=$(pwd)/goodman_pipeline/data/dcr-source/dcr
+SOURCE_DIR=$(pwd)/goodman_pipeline/data/dcr_source/dcr
 
 
 
@@ -10,8 +10,8 @@ then
 	echo 'You do not have any virtual environment activated'
 
 else
-	ENV_NAME=$(conda info | grep 'active environment' | sed 's/\<active environment\>//g' | sed "s/[: ]//g")
-	ENV_PATH=$(conda info | grep 'active env location' | sed 's/\<active env location\>//g' | sed "s/[: ]//g")
+	ENV_NAME=$(conda info | grep 'active environment' | sed 's/active environment//g' | sed "s/[: ]//g")
+	ENV_PATH=$(conda info | grep 'active env location' | sed 's/active env location//g' | sed "s/[: ]//g")
 	echo "Using Virtual Environment: " $ENV_NAME
 	echo "Environment path information: " $ENV_PATH
 	if [ -d $SOURCE_DIR ]

setup.cfg

@@ -1,16 +1,16 @@
 [build_docs]
-source-dir = docs
-build-dir = docs/_build
+source_dir = docs
+build_dir = docs/_build
 all_files = 1
 
 [build_sphinx]
 project = 'Goodman Pipeline'
-source-dir = docs
-build-dir = docs/_build
+source_dir = docs
+build_dir = docs/_build
 
 [upload_docs]
-upload-dir = docs/_build/html
-show-response = 1
+upload_dir = docs/_build/html
+show_response = 1
 
 [metadata]
 package_name = goodman_pipeline

setup.py

@@ -145,8 +145,8 @@ def create_version_py(packagename, version, source_dir='.'):
     package_data={'goodman_pipeline': ['data/params/dcr.par',
                                        'data/params/*.json_output',
                                        'data/ref_comp/*fits',
-                                       'data/dcr-source/README.md',
-                                       'data/dcr-source/dcr/*',
+                                       'data/dcr_source/README.md',
+                                       'data/dcr_source/dcr/*',
                                        'data/test_data/master_flat/*',
                                        'data/test_data/wcs_data/*']},
 

travis_install_dcr.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-SOURCE_DIR=$(pwd)/goodman_pipeline/data/dcr-source/dcr
+SOURCE_DIR=$(pwd)/goodman_pipeline/data/dcr_source/dcr
 
 BINARY_FOLDER=$VIRTUAL_ENV/bin