Merge pull request #415 from GeminiDRSoftware/conda_forge_master

Update `master` tests/docs to use conda-forge instead of Astroconda

.github/workflows/unit-tests.yml

@@ -32,8 +32,7 @@ jobs:
       - uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
-          channels: http://ssb.stsci.edu/astroconda
-          channel-priority: disabled
+          channels: conda-forge
           python-version: ${{ matrix.python-version }}
           use-only-tar-bz2: true
 

.jenkins/scripts/download_and_install_anaconda.sh

@@ -2,35 +2,42 @@
 
 echo "Checking (Ana/Mini)Conda installation at ${JENKINS_CONDA_HOME}"
 
+mkdir -p "${TMPDIR}"  # otherwise micromamba (miniforge install) crashes
+
 ## Remove anaconda to replace with miniconda
 if [ -d "${JENKINS_CONDA_HOME}/bin/anaconda" ]; then
     rm -Rf ${JENKINS_CONDA_HOME}
 fi
 
-LINUX_URL="https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh"
-MACOS_URL="https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh"
+LINUX_URL="https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh"
+MACOS_URL="https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh"
 
 if [[ "$(uname)" == "Darwin" ]]; then
     CONDA_URL="${MACOS_URL}"
 elif [[ "$(expr substr $(uname -s) 1 5)" == "Linux" ]]; then
     CONDA_URL="${LINUX_URL}"
 fi
 
+env
+
 if ! [[ "$(command -v conda)" ]]; then
     echo "\n\n   Conda is not installed - Downloading and installing\n\n"
-    curl "${CONDA_URL}" --output Miniconda3-latest.sh --silent
+    curl -L "${CONDA_URL}" --output Miniforge3-latest.sh --silent
 
-    chmod a+x Miniconda3-latest.sh
-    ./Miniconda3-latest.sh -u -b -p ${JENKINS_CONDA_HOME}
+    chmod a+x Miniforge3-latest.sh
+    ./Miniforge3-latest.sh -u -b -p ${JENKINS_CONDA_HOME}
 else
   echo "\n\n   Conda is already installed --- Skipping step.\n\n"
 fi
 
 echo ${PATH}
 which conda
 conda update --quiet conda
-conda config --add channels http://ssb.stsci.edu/astroconda
-conda config --add channels http://astroconda.gemini.edu/public/noarch
-conda config --set channel_priority false
-conda config --set restore_free_channel true
+# These 2 channels need removing if testing old branches has reinstated them:
+conda config --remove channels http://ssb.stsci.edu/astroconda || :
+conda config --remove channels http://astroconda.gemini.edu/public/noarch || :
+conda config --add channels conda-forge
+conda config --add channels http://astroconda.gemini.edu/public
+conda config --set channel_priority true
+conda config --set restore_free_channel false
 conda env list

README.md

@@ -26,13 +26,13 @@ data for science purposes, please continue to use the [Gemini IRAF package](http
 To install DRAGONS:
 
 ```
-$ conda create -n dragons python=3.7 dragons stsci
+$ conda create -n dragons python=3.7 dragons ds9
 ```
 
 You might need to add two relevant conda channels if you haven't already:
 
 ```
-$ conda config --add channels http://ssb.stsci.edu/astroconda
+$ conda config --add channels conda-forge
 $ conda config --add channels http://astroconda.gemini.edu/public
 ```
 

astrodata/doc/usermanual/intro.rst

@@ -56,7 +56,7 @@ Installing Astrodata
 
 The |astrodata| package has a few dependencies, |astropy|, |numpy| and others.
 The best way to get everything you need is to install Anaconda_, and the
-|dragons| stack from the AstroConda channel.
+|dragons| stack from conda-forge and Gemini's public conda channel.
 
 |astrodata| itself is part of |DRAGONS|. It is available from the
 repository, as a tar file, or as a conda package. The bare |astrodata| package
@@ -86,12 +86,12 @@ repository, the tar file or the conda package.
     $ conda init
 
 #. Set up conda channels.
-    Configure the ``conda`` package manager to look in the AstroConda channel
-    hosted by STScI, and in the GEMINI Conda Channel. This is a one-time step.
-    It affects current and future Anaconda installations belonging to the same
-    user on the same machine.::
+    Configure the ``conda`` package manager to look in conda-forge, and in the
+    GEMINI Conda Channel. This is a one-time step. It affects current and
+    future Anaconda installations belonging to the same user on the same
+    machine.::
 
-    $ conda config --add channels http://ssb.stsci.edu/astroconda
+    $ conda config --add channels conda-forge
     $ conda config --add channels http://astroconda.gemini.edu/public
 
 #. Create an environment.
@@ -107,7 +107,7 @@ repository, the tar file or the conda package.
     recommend that you use this specific version of Python with DRAGONS.
     ::
 
-    $ conda create -n dragons python=3.7 dragons stsci
+    $ conda create -n dragons python=3.7 dragons ds9
 
 
 #. Activate your new virtual environment.

doc/DRAGONS/testing.rst

@@ -231,10 +231,6 @@ on Python 3.7:
    # specifying the environment with an environment variable:
    $ TOXENV=py37-unit tox
 
-.. note::
-    Since we use the `astroconda <http://ssb.stsci.edu/astroconda>`_ channel
-    which does not have packages for Python 3.8 and 3.9, tox can currently
-    only be used with Python 3.7.
 
 Pinpointing Tests
 -----------------

geminidr/doc/tutorials/F2Img-DRTutorial/01_introduction.rst

@@ -39,8 +39,6 @@ been installed. If you have an error message, make sure:
 
     - A Conda Virtual Environment is properly created and is active;
 
-    - AstroConda (STScI) is properly installed within the Virtual Environment;
-
     - DRAGONS was successfully installed within the Conda Virtual Environment;
 
 

geminidr/doc/tutorials/GMOSImg-DRTutorial/01_introduction.rst

@@ -41,8 +41,6 @@ be installed. If you have an error message, make sure:
 
     - A Conda Virtual Environment is properly created and is active;
 
-    - AstroConda (STScI) is properly installed within the Virtual Environment;
-
     - DRAGONS was successfully installed within the Conda Virtual Environment;
 
 

geminidr/doc/tutorials/GSAOIImg-DRTutorial/01_introduction.rst

@@ -39,8 +39,6 @@ be installed. If you have an error message, make sure:
 
     - A Conda Virtual Environment is properly created and is active;
 
-    - AstroConda (STScI) is properly installed within the Virtual Environment;
-
     - DRAGONS was successfully installed within the Conda Virtual Environment;
 
 .. _datasetup:

recipe_system/doc/rs_UsersManual/install.rst

@@ -89,13 +89,12 @@ anaconda.  To activate or deactivate Anaconda manually::
     $ conda activate
     $ conda deactivate
 
-Now that Anaconda works, we add the needed astronomy software.  Add the
-Astroconda channel and the Gemini channel.  Those channels host
-the conda astronomy packages.
+Now that Anaconda works, we add the needed astronomy software.  Add conda-forge
+and the Gemini channel.  Those channels host the conda astronomy packages.
 
 ::
 
-    $ conda config --add channels http://ssb.stsci.edu/astroconda
+    $ conda config --add channels conda-forge
     $ conda config --add channels http://astroconda.gemini.edu/public
 
 The next step is to create a virtual environment and install the DRAGONS
@@ -105,14 +104,7 @@ Python 3.7.
 
 ::
 
-    $ conda create -n dragons python=3.7 dragons
-
-    Or, to include things like ds9
-
-    $ conda create -n dragons python=3.7 dragons stsci
-
-Most users will probably want to install the extra astronomy tools that come
-with the ``stsci`` conda package.
+    $ conda create -n dragons python=3.7 dragons ds9
 
 To use this environment, activate it::
 
@@ -124,16 +116,13 @@ command to your ``.bash_profile``, after the "conda init" block.
 
 .. note::
     As a side note, if you are going to use PyRAF regularly, for example to
-    reduce Gemini data not yet supported in DRAGONS, you should be installing
-    Python 2.7 **as well** in a different environment, along with the ``gemini``,
-    ``iraf-all`` and ``pyraf-all`` conda packages.  Do not use PyRAF from the
-    Python 3 environment; PyRAF is very slow under Python 3.
+    reduce Gemini data not yet supported in DRAGONS, you should install the
+    ``iraf-all`` and ``pyraf-all`` conda packages as well.
 
-    $ conda create -n geminiconda python=2.7 iraf-all pyraf-all stsci gemini
+    $ conda create -n geminiconda python=3.7 iraf-all pyraf-all ds9 dragons
 
-    DRAGONS and the Recipe System do not need IRAF, PyRAF.  Only DRAGONS v2
-    is compatible with Python 2.7.   See the Gemini website for information on
-    how to configure IRAF (|geminiiraf_link|)
+    DRAGONS and the Recipe System do not need IRAF or PyRAF, however. See the
+    Gemini website for information on how to configure IRAF (|geminiiraf_link|)
 
 .. _configure::
 

tox.ini

@@ -1,6 +1,6 @@
 [tox]
 envlist =
-    py{36,37,38,39}-{unit,f2,gsaoi,niri,gnirs,gmosls,integ,reg,slow}
+    py{37,38,39,310,311}-{unit,f2,gsaoi,niri,gnirs,gmosls,integ,reg,slow}
     codecov
     check
     docs-{astrodata}
@@ -21,26 +21,43 @@ passenv =
     MPLBACKEND
     TMPDIR
 conda_deps =
+    asdf>=2.7,!=2.10.0
     astropy>=4.3
-    astroquery
-    cython
-    future
-    gwcs
-    Jinja2
-    matplotlib
-    numpy
-    pytest
-    scipy
-    sextractor
-    specutils
-    sqlalchemy
+    astroquery>=0.4
+    astroscrappy>=1.1
+    bokeh>=2.3
+    bottleneck>=1.2
+    coverage
+    cython>=0.29
+    docutils>=0.15
+    future>=0.17
+    gwcs>=0.15
+    holoviews>=1.14
+    jinja2>=3.0
+    jsonschema>=3.0
+    matplotlib>=3.1
+    numpy>=1.17
+    objgraph>=3.5
+    psutil>=5.6  # only used by adcc?
+    pyerfa>=1.7
+    pytest>=5.2
+    python-dateutil>=2.5.3
+    requests>=2.22
+    scipy>=1.3
+    sextractor>=2.8.6
+    specutils>=1.1,<1.9  # the 1.9.1 conda package has incorrect constraints
+    sqlalchemy>=1.3
 conda_channels =
-    http://ssb.stsci.edu/astroconda
+    http://astroconda.gemini.edu/public
+    conda-forge
+conda_create_args =
+    --override-channels
+conda_install_args =
+    --override-channels
 extras =
     test
     docs: docs
 deps =
-    coverage
     .jenkins/local_calibration_manager/GeminiObsDB-1.0.22-py3-none-any.whl
     .jenkins/local_calibration_manager/GeminiCalMgr-1.1.12-py3-none-any.whl
     git+https://github.com/GeminiDRSoftware/pytest_dragons.git@v1.0.4#egg=pytest_dragons
@@ -51,7 +68,6 @@ commands =
     which python
     which pip
     which pytest
-    pip install git+https://github.com/astropy/astroscrappy.git@1.1.0#egg=astroscrappy
     pip install git+https://github.com/GeminiDRSoftware/AstroFaker#egg=AstroFaker
     conda list
     unit: python -m coverage run --rcfile={toxinidir}/.coveragerc -m pytest -v --dragons-remote-data --durations=20 -m "not integration_test and not gmosls and not f2 and not f2ls and not f2image and not gsaoi and not gsaoiimage and not niri and not nirils and not niriimage and not gnirs and not gnirsls and not gnirsimage and not wavecal and not regression and not slow" {posargs:astrodata geminidr gemini_instruments gempy recipe_system}