Update prject to lastest changes

.github/workflows/python-package.yml

@@ -15,12 +15,12 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8]
+        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

@@ -7,11 +7,12 @@ __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/*
 .tmp/*
 .tox/*
 goodman_pipeline.egg-info/*
+*.DS_Store

.readthedocs.yml

@@ -1,14 +1,17 @@
 version: 2
 
+build:
+  os: ubuntu-lts-latest
+  tools:
+    python: "mambaforge-22.9"
+
+
 sphinx:
     configuration: docs/conf.py
 
 formats: all
 
-
-
 python:
-    version: 3.5
     install:
         - method: pip
           path: .

README.md

@@ -1,15 +1,14 @@
 # Goodman High Throughput Spectrograph Data Reduction Pipeline
 
-![Goodman Pipeline](https://github.com/soar-telescope/goodman_pipeline/workflows/Goodman%20Pipeline/badge.svg?branch=master)
+![Goodman Pipeline](https://github.com/soar-telescope/goodman_pipeline/actions/workflows/python-package.yml/badge.svg)
 [![codecov](https://codecov.io/gh/soar-telescope/goodman_pipeline/branch/main/graph/badge.svg)](https://codecov.io/gh/soar-telescope/goodman_pipeline)
 [![Documentation Status](https://readthedocs.org/projects/goodman/badge/?version=latest)](http://goodman.readthedocs.io/en/latest/?badge=latest)
 [![pypi](https://img.shields.io/pypi/v/goodman_pipeline.svg?style=flat)](https://pypi.org/project/goodman-pipeline/)
 [![astropy](http://img.shields.io/badge/powered%20by-AstroPy-orange.svg?style=flat)](http://www.astropy.org/)
 
 
 ![Upload to PYPI](https://github.com/soar-telescope/goodman_pipeline/workflows/Upload%20to%20PYPI/badge.svg)
-[![Total alerts](https://img.shields.io/lgtm/alerts/g/soar-telescope/goodman_pipeline.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/soar-telescope/goodman_pipeline/alerts/)
-[![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/soar-telescope/goodman_pipeline.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/soar-telescope/goodman_pipeline/context:python)
+
 
 ## Overview
 The Goodman High Throughput Spectrograph (Goodman HTS) Data-Reduction Pipeline

docs/_common_issues.rst

@@ -0,0 +1,48 @@
+.. _common_issues:
+
+Common issues
+*************
+
+No comparison lamps were found
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The latest version may introduce changes to wavelength solutions. To
+view the current list of available modes and lamps, please refer to the
+`GitHub repository <https://github.com/soar-telescope/goodman_pipeline/tree/main/goodman_pipeline/data/ref_comp>`_.
+
+If your lamp, filter, or mode is not included in the repository mentioned
+above, ``redspec`` will not work as expected. This is particularly common
+with custom modes of the |pipeline full name|. You may encounter the following
+error after running ``redspec``:
+
+.. code-block:: console
+
+    $ redspec
+    ፧
+    [15:02:49][W]: No comparison lamps were provided for file ecfzst_0001_science.fits
+
+This error occurs because the |pipeline full name| relies on specific keywords to
+extract spectra, such as:
+
+.. _`table lamp key`:
+
+.. table:: Keywords that are used to produce a wavelength solution.
+
+    ========== =============================================================
+     Keyword    Purpose
+    ========== =============================================================
+     LAMP_HGA   Indicates if HgAr lamp is used.
+     LAMP_NE    Indicates if Ne lamp is used.
+     LAMP_AR    Indicates if Ar lamp is used.
+     LAMP_FE    Indicates if Fe lamp is used.
+     LAMP_CU    Indicates if Cu lamp is used.
+     WAVMODE    Slit and mode configuration.
+    ========== =============================================================
+
+Multiple spectra output
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+When taking multiple ``ARC`` images during your observation run, they will be linked
+with your science data. This means that if you capture several lamp files,
+they will be processed alongside the science images, potentially resulting
+in multiple outputs of the same spectrum.

docs/_file_prefixes.rst

@@ -45,19 +45,15 @@ So what does all those letter mean? Here is a table to explain it.
 
 So, for an original file named ``file.fits``:
 
-  ``o_file.fits``
-
-Means the file have been overscan corrected while
-
-  ``eczsto_file.fits``
+  ``eczst_file.fits``
 
 Means the spectrum has been extracted to a 1D  file but the file has not been
 flat fielded (``f`` missing).
 
 Ideally after running ``redccd`` the file should be named:
 
-  ``cfzsto_file.fits``
+  ``cfzst_file.fits``
 
 And after running ``redspec``:
 
-  ``wecfzsto_file.fits``
+  ``wecfzst_file.fits``

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/_running_prepare_data_for_reduction.rst

@@ -25,6 +25,10 @@ need to change the following keywords.
   ``SYZY_400`` becomes ``400_SYZY``.
 - ``WAVMODE``: Replace whitespace with underscore and all letters are capitalized.
   For instance. ``400 m1`` becomes ``400_M1``.
+- ``INSTRUME``: Instead of using the classical keywords 'Goodman Spectro' and
+  'Goodman Imaging', the AEON standard keywords ``ghts_red`` and ``ghts_blue``
+  will be used for spectroscopy, and ``ghts_red_imager`` and ``ghts_blue_imager``
+  for imaging. This is an exception of the upper case rule.
 
 .. note::
 

docs/_running_redspec.rst

@@ -27,13 +27,14 @@ behavior for every user or science case, we have implemented a set of
   is *current working directory*.
 - ``--proc-path <path>`` Folder were processed data will be stored. Default
   is *current working directory*.
-- ``--search-pattern <pattern>`` Prefix for picking up files. Default
-  ``cfzst``. See :ref:`file-prefixes`.
-- ``--output-prefix <prefix>`` Prefix to be added to calibrated spectrum.
+- ``--search-pattern <pattern>`` Prefix for picking up files. Default is
+  ``cfzst-``. See :ref:`file-prefixes`.
+- ``--output-prefix <prefix>`` Prefix to be added to calibrated spectrum. Default is
+  ``w-``. See :ref:`file-prefixes`.
 - ``--extraction <method>`` Select the :ref:`extraction-methods`. The only one
   implemented at the moment is ``fractional`` .
 - ``--fit-targets-with {moffat, gaussian}`` Model to fit peaks on spatial profile
-  while searching for spectroscopic targets.
+  while searching for spectroscopic targets. Default ``moffat``.
 - ``--target-min-width <target min width>`` Minimum profile width for fitting the spatial axis of spectroscopic targets.
   If fitting a Moffat it will be reflected as the FWHM attribute of the fitted model and if fitting a Gaussian it will
   be reflected as the STDDEV attribute of the Gaussian model.

docs/change_history.rst

@@ -1,6 +1,30 @@
 Change History
 ##############
 
+
+.. _v1.3.8:
+
+V1.3.8 Not Released
+^^^^^^^^^^^^^^^^^^^
+
+- Documentation update
+- Fix DCR bug that was present when called from CLI.
+- Fixed Bug when using relative path for selecting master flat
+
+
+.. _v1.3.7:
+
+V1.3.7 17-08-2023
+^^^^^^^^^^^^^^^^^
+
+- Updated documentation theme to allow dark mode
+- Removed python 3.6 and 3.8 from testing and added 3.9 and 3.10
+- Unfixed numpy version
+- Removed testing with conda on github action because it only added complexity
+- Added 3 seconds timeout to request to github to validate version and check if running version is latest
+- Added correct exception handler in case the http request timed out.
+
+
 .. _v1.3.6:
 
 V1.3.6 25-03-2022
@@ -336,4 +360,4 @@ V1.0.1 xx-xx-2018
 V1.0.0 29-04-2018
 ^^^^^^^^^^^^^^^^^
 
-- First production ready release
+- First production ready release

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.
@@ -109,7 +109,7 @@
 #
 # html_theme = 'bootstrap-astropy'
 
-html_theme = 'sphinx_rtd_theme'
+html_theme = 'pydata_sphinx_theme'
 
 html_logo = '_static/soar_logo.png'
 

docs/index.rst

@@ -12,7 +12,7 @@
 Welcome to the Goodman HTS Pipeline Documentation
 =================================================
 
-.. image:: https://github.com/soar-telescope/goodman_pipeline/workflows/Goodman%20Pipeline/badge.svg?branch=master
+.. image:: https://github.com/soar-telescope/goodman_pipeline/actions/workflows/python-package.yml/badge.svg
     :alt: Goodman Pipeline
 .. image:: https://codecov.io/gh/soar-telescope/goodman_pipeline/branch/main/graph/badge.svg
     :target: https://codecov.io/gh/soar-telescope/goodman_pipeline
@@ -25,10 +25,6 @@ Welcome to the Goodman HTS Pipeline Documentation
     :target: http://www.astropy.org/
 
 
-.. image:: https://img.shields.io/lgtm/alerts/g/soar-telescope/goodman_pipeline.svg?logo=lgtm&logoWidth=18
-    :target: https://lgtm.com/projects/g/soar-telescope/goodman_pipeline/alerts/
-.. image:: https://img.shields.io/lgtm/grade/python/g/soar-telescope/goodman_pipeline.svg?logo=lgtm&logoWidth=18
-    :target: https://lgtm.com/projects/g/soar-telescope/goodman_pipeline/context:python
 
 This is the User Manual for the *Goodman Spectroscopic Data Reduction
 Pipeline*. It provides an overview of the pipeline's main features,

docs/usage.rst

@@ -34,9 +34,10 @@ Getting Help.
 
 .. include:: _extraction_methods.rst
 
-
 .. include:: _file_prefixes.rst
 
 .. include:: _file_suffixes.rst
 
 .. include:: _shortcuts.rst
+
+.. include:: _common_issues.rst