Merge branch 'release/3.2.x'

GeminiDRSoftware · Apr 16, 2024 · d5cb575 · d5cb575
2 parents bee8e73 + bf3b6c4
commit d5cb575
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diff --git a/.github/workflows/unit-tests.yml b/.github/workflows/unit-tests.yml
@@ -19,7 +19,7 @@ jobs:
       - uses: actions/checkout@v2
 
       - name: Cache conda packages and test files
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         env:
           # Increase this value to reset cache
           CACHE_NUMBER: 0
@@ -29,12 +29,11 @@ jobs:
             ~/dragons_tests
           key: ${{ runner.os }}-${{ env.CACHE_NUMBER }}
 
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           channels: conda-forge
           python-version: ${{ matrix.python-version }}
-          use-only-tar-bz2: true
 
       - name: Conda info
         shell: bash -l {0}
@@ -53,4 +52,4 @@ jobs:
       - name: Run Tox
         shell: bash -l {0}
         run: |
-          tox -e py310-unit -v
+          tox -r -e py310-unit -v
diff --git a/.gitignore b/.gitignore
@@ -157,3 +157,6 @@ dmypy.json
 **/.adcc
 **/dragons_test_inputs
 **/spec_data.json
+
+# VSCode settings
+.vscode/settings.json
diff --git a/.jenkins/local_calibration_manager/GeminiCalMgr-1.1.23-py3-none-any.whl b/.jenkins/local_calibration_manager/GeminiCalMgr-1.1.23-py3-none-any.whl
diff --git a/.jenkins/local_calibration_manager/GeminiObsDB-1.0.29-py3-none-any.whl b/.jenkins/local_calibration_manager/GeminiObsDB-1.0.29-py3-none-any.whl
diff --git a/Jenkinsfile b/Jenkinsfile
@@ -20,14 +20,15 @@ def runtests_niri    = 1
 def runtests_gsaoi   = 1
 def runtests_gnirs   = 1
 def runtests_wavecal = 1
+def runtests_ghost   = 1
 
 pipeline {
 
     agent any
 
     //triggers {
-    //   // Polls Source Code Manager every four hours
-    //    pollSCM('*/15 * * * *')
+    //   //Polls Source Code Manager every 15 mins
+    //   pollSCM('*/15 * * * *')
     //}
 
     options {
@@ -418,7 +419,7 @@ pipeline {
                     agent { label "master" }
                     environment {
                         MPLBACKEND = "agg"
-                        DRAGONS_TEST_OUT = "regression_tests_outputs"
+                        DRAGONS_TEST_OUT = "slow_tests_outputs"
                         TOX_ARGS = "astrodata geminidr gemini_instruments gempy recipe_system"
                         TMPDIR = "${env.WORKSPACE}/.tmp/slow/"
                     }
@@ -446,6 +447,43 @@ pipeline {
                         }
                     } // end post
                 } // end stage
+
+                stage('GHOST Tests') {
+                    when {
+                        expression { runtests_gnirs == 1 }
+                    }
+
+                    agent { label "master" }
+                    environment {
+                        MPLBACKEND = "agg"
+                        DRAGONS_TEST_OUT = "ghost_tests_outputs"
+                        TOX_ARGS = "astrodata geminidr gemini_instruments gempy recipe_system"
+                        TMPDIR = "${env.WORKSPACE}/.tmp/ghost/"
+                    }
+                    steps {
+                        echo "Running build #${env.BUILD_ID} on ${env.NODE_NAME}"
+                        checkout scm
+                        echo "${env.PATH}"
+                        sh '.jenkins/scripts/setup_dirs.sh'
+                        echo "GHOST tests"
+                        sh 'tox -e py310-ghost -v -- --basetemp=${DRAGONS_TEST_OUT} --junit-xml reports/ghost_results.xml ${TOX_ARGS}'
+                        echo "Reporting coverage"
+                        sh 'tox -e codecov -- -F ghost'
+                    } // end steps
+                    post {
+                        always {
+                            junit (
+                                allowEmptyResults: true,
+                                testResults: '.tmp/py310-ghost/reports/*_results.xml'
+                            )
+                            echo "Deleting GHOST Tests workspace ${env.WORKSPACE}"
+                            cleanWs()
+                            dir("${env.WORKSPACE}@tmp") {
+                              deleteDir()
+                            }
+                        }
+                    } // end post
+                } // end stage
             } // end parallel
         }
 

diff --git a/LICENSE b/LICENSE
@@ -6,7 +6,7 @@ whether written by AURA or third parties.
 
 -----
 
-Copyright (C) 2014-2021 Association of Universities for Research in Astronomy, Inc. (AURA)
+Copyright (C) 2014-2024 Association of Universities for Research in Astronomy, Inc. (AURA)
 
 Redistribution and use in source and binary forms, with or without modification,
 are permitted provided that the following conditions are met:

diff --git a/README.md b/README.md
@@ -11,23 +11,23 @@
 </table>
 
 # Current Status
-**The stable version is v3.1.0.**  
+**The stable version is v3.2.0.**  
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7776065.svg)](https://doi.org/10.5281/zenodo.7776065) 
-DRAGONS is distributed as a conda package, *dragons*, and it is 
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10841622.svg)](https://doi.org/10.5281/zenodo.10841622) DRAGONS is distributed as a conda package, *dragons*, and it is 
 included in the conda *gemini* stack.
 
-Version 3.1 is recommend for the reduction of **imaging** data from Gemini's
-current facility instruments: GMOS, NIRI, Flamingos-2, and GSAOI, and for the
-reduction of GMOS longslit spectroscopy data.
+Version 3.2 is recommend for the reduction of **imaging** data from Gemini's
+current facility instruments: GMOS, NIRI, Flamingos-2, and GSAOI, for the
+reduction of GMOS longslit spectroscopy data, and the reduction of GHOST data.
 
 To reduce other types of Gemini spectroscopy data, please continue to use 
-the [Gemini IRAF package](https://gemini.edu/observing/phase-iii/reducing-data/gemini-iraf-data-reduction-software).
+the [Gemini IRAF package](https://www.gemini.edu/observing/phase-iii/reducing-data/gemini-iraf-data-reduction-software).
 
 To install DRAGONS:
 
 ```
-`$ conda create -n dragons python=3.10 dragons ds9
+$ conda create -n dragons python=3.10 dragons ds9
 ```
 
 You might need to add two relevant conda channels if you haven't already:
@@ -38,7 +38,7 @@ $ conda config --add channels http://astroconda.gemini.edu/public
 ```
 
 
-A list of changes since 3.0 can be found in the [Change Logs](https://dragons.readthedocs.io/en/v3.1.0/changes.html).
+A list of changes since 3.1 can be found in the [Change Logs](https://dragons.readthedocs.io/en/v3.2.0/changes.html).
 
 ---
 # What is DRAGONS
@@ -51,9 +51,9 @@ reduction of Gemini data.
 ---
 
 # Documentation
-Documentation on DRAGONS v3.1 is available on "readthedocs" at:
+Documentation on DRAGONS v3.2 is available on "readthedocs" at:
 
-* https://dragons.readthedocs.io/en/v3.1.0/
+* https://dragons.readthedocs.io/en/v3.2.0/
 
 There your will find manuals for Astrodata and the Recipe System, and hands-on
 tutorials on reducing Gemini imaging data with DRAGONS.
@@ -66,21 +66,20 @@ manuals.
 
 ---
 
-# Citing DRAGONS
-
-If you are using DRAGONS for your project, we ask that you please cite the 
-following paper:
-
-* [K. Labrie et al 2023 Res. Notes AAS 7 214](https://iopscience.iop.org/article/10.3847/2515-5172/ad0044) ([BibTex](https://iopscience.iop.org/export?type=article&doi=10.3847/2515-5172/ad0044&exportFormat=iopexport_bib&exportType=abs&navsubmit=Export+abstract))
-
-The DOI for DRAGONS version 3.1.0 is:
+# Setting up a development environment
 
-* [10.5281/zenodo.7776065](https://zenodo.org/record/7776065) ([BibTex](https://zenodo.org/record/7776065/export/hx))
-
-If you are using AASTeX and plan to submit an article to one of the AAS journals,
-we recommend adding a `\software` tag to your manuscript that cites DRAGONS and
-the specific version you have used. For example:
+To run checkouts, first set up a development conda environment.  This is what
+we are using at this time for the `master` branch and the `release/3.2.x` 
+branches.
 
 ```
-\software{DRAGONS \citep{dragonsRNAAS_2023}, \cite[Version 3.1.0]{dragons3.1.0}
-```
+$ conda create -n dgdev3.10_20240401 python=3.10 astropy=6 astroquery matplotlib numpy psutil pytest python-dateutil requests scikit-image scipy sextractor sqlalchemy ds9 gwcs specutils sphinx sphinx_rtd_theme bokeh holoviews cython future astroscrappy=1.1 fitsverify imexam
+$ conda activate dgdev3.10_20240401
+$ pip install git+https://github.com/GeminiDRSoftware/GeminiObsDB.git@release/1.0.x
+$ pip install git+https://github.com/GeminiDRSoftware/GeminiCalMgr.git@release/1.1.x
+```
+Dependencies change all the time and can break the development environment
+or cause problems when conda tries to find a solution for the dependencies. 
+This not guaranteed to work flawlessly, you might have to adjust version
+requirements.
+
diff --git a/astrodata/_version.py b/astrodata/_version.py
@@ -7,8 +7,8 @@
 # --- Setup Version Here ---
 API = 3
 FEATURE = 2
-BUG = 0
-TAG = ''
+BUG = 1
+TAG = 'dev'
 
 
 def version(short=False, tag=TAG):

diff --git a/astrodata/doc/.readthedocs.yaml b/astrodata/doc/.readthedocs.yaml
@@ -0,0 +1,32 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+    # You can also specify other tool versions:
+    # nodejs: "19"
+    # rust: "1.64"
+    # golang: "1.19"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: astrodata/doc/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+# formats:
+#    - pdf
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - requirements: requirements.txt
+   - requirements: doc/requirements.txt
+   - method: pip
+     path: .
diff --git a/astrodata/doc/cheatsheet.rst b/astrodata/doc/cheatsheet.rst
@@ -13,7 +13,7 @@ Cheat Sheet
 A data package is available for download if you wish to run the examples
 included in this cheat sheet.  Download it at:
 
-    `<http://www.gemini.edu/sciops/data/software/datapkgs/ad_usermanual_datapkg-v1.tar>`_
+    `<https://www.gemini.edu/sciops/data/software/datapkgs/ad_usermanual_datapkg-v1.tar>`_
 
 To unpack::
 

diff --git a/astrodata/doc/conf.py b/astrodata/doc/conf.py
@@ -49,7 +49,7 @@
 
 # General information about the project.
 project = 'Astrodata Manual'
-copyright = '2023, Association of Universities for Research in Astronomy'
+copyright = '2024, Association of Universities for Research in Astronomy'
 author = 'DRAGONS Team'
 
 # The version info for the project you're documenting, acts as replacement for
@@ -58,10 +58,10 @@
 #
 # The short X.Y version.
 version = '3.2'
-# The ull version, including alpha/beta/rc tags.
-#release = '3.1.x'
+# The full version, including alpha/beta/rc tags.
+#release = '3.2.x'
 #rtdurl = 'release-'+release
-#release = '3.1.0'
+#release = '3.2.0'
 #rtdurl = 'v'+release
 rtdurl = 'latest'
 
@@ -76,7 +76,7 @@
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
 #
-today = 'April 2023'
+today = 'April 2024'
 #
 # Else, today_fmt is used as the format for a strftime call.
 #
@@ -458,6 +458,8 @@ def setup(app):
 .. |RSProgManual| replace:: :raw-html:`<a href="http://dragons-recipe-system-programmers-manual.readthedocs.io/en/{v}/">Recipe System Programmer Manual</a>`
 .. |RSUserManual| replace:: :raw-html:`<a href="http://dragons-recipe-system-users-manual.readthedocs.io/en/{v}/">Recipe System User Manual<a>`
 
+.. |RSUserInstall|  replace:: :raw-html:`<a href="http://dragons-recipe-system-users-manual.readthedocs.io/en/{v}/install.html">Installation Guide</a>`
+
 
 """.format(v = rtdurl)
 
diff --git a/astrodata/doc/usermanual/data.rst b/astrodata/doc/usermanual/data.rst
@@ -674,7 +674,7 @@ add a variance plane to our raw data frame.
     >>> # Here we work on the NDAstroData object to have the variance
     >>> # trimmed automatically to the same size as the science array.
     >>> # To reassign the cropped NDAstroData, we use the reset() method.
-    >>> ad[0].reset(ad[0].nddata[datasec.y1:datasec.y2, datasec.x1:datasec.x2]
+    >>> ad[0].reset(ad[0].nddata[datasec.y1:datasec.y2, datasec.x1:datasec.x2])
 
     >>> # Now look at the dimensions of the first extension, science
     >>> # and variance.  That extension is smaller than the others.
@@ -771,9 +771,9 @@ attention.
     >>> intensity = adcube[0].data[:, 24, 13]   # (wlen, y, x)
 
     # We plot
-    plt.clf()
-    plt.plot(wavelengths, intensity)
-    plt.show()
+    >>> plt.clf()
+    >>> plt.plot(wavelengths, intensity)
+    >>> plt.show()
 
 
 Plot Data
@@ -874,7 +874,7 @@ what ``imexam`` has to offer.
     >>> ds9.scale('zscale')
 
     # Run in interactive mode.  Try the various commands.
-   >>> ds9.imexam()
+    >>> ds9.imexam()
 
     # Use the programmatic interface
     # First initialize an Imexamine object.