Merge branch 'sara-nl-20221017182151_new_pr_JupyterHub300' into develop

Resolving merge conflicts

.github/workflows/linting.yml

@@ -0,0 +1,20 @@
+name: Static Analysis
+on: [push, pull_request]
+jobs:
+  python-linting:
+    runs-on: ubuntu-20.04
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+
+    - name: install Python packages
+      run: |
+        pip install --upgrade pip
+        pip install --upgrade flake8
+
+    - name: Run flake8 to verify PEP8-compliance of Python code
+      run: flake8

.github/workflows/unit_tests.yml

@@ -0,0 +1,187 @@
+name: easyconfigs unit tests
+on: [push, pull_request]
+jobs:
+  test-suite:
+    runs-on: ubuntu-20.04
+    strategy:
+      matrix:
+        python: [2.7, 3.6]
+        modules_tool: [Lmod-7.8.22, Lmod-8.6.8]
+        module_syntax: [Lua, Tcl]
+        # exclude some configurations: only test Tcl module syntax with Lmod 8.x and Python 2.7 & 3.6
+        exclude:
+          - modules_tool: Lmod-7.8.22
+            module_syntax: Tcl
+      fail-fast: false
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0 # Required for git merge-base to work
+
+    - name: Cache source files in /tmp/sources
+      id: cache-sources
+      uses: actions/cache@v2
+      with:
+        path: /tmp/sources
+        key: eb-sourcepath
+
+    - name: set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{matrix.python}}
+        architecture: x64
+
+    - name: install OS & Python packages
+      run: |
+        # disable apt-get update, we don't really need it,
+        # and it does more harm than good (it's fairly expensive, and it results in flaky test runs)
+        # sudo apt-get update
+        # for modules tool
+        sudo apt-get install lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev
+        # fix for lua-posix packaging issue, see https://bugs.launchpad.net/ubuntu/+source/lua-posix/+bug/1752082
+        # needed for Ubuntu 18.04, but not for Ubuntu 20.04, so skipping symlinking if posix.so already exists
+        if [ ! -e /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so ] ; then
+            sudo ln -s /usr/lib/x86_64-linux-gnu/lua/5.2/posix_c.so /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so
+        fi
+        # for testing OpenMPI-system*eb we need to have Open MPI installed
+        sudo apt-get install libopenmpi-dev openmpi-bin
+        # required for test_dep_graph
+        pip install pep8 python-graph-core python-graph-dot
+
+    - name: install EasyBuild framework
+      run: |
+          cd $HOME
+          # first determine which branch of easybuild-framework repo to install
+          BRANCH=develop
+          if [ "x$GITHUB_BASE_REF" = 'xmain' ]; then BRANCH=main; fi
+          if [ "x$GITHUB_BASE_REF" = 'x4.x' ]; then BRANCH=4.x; fi
+          echo "Using easybuild-framework branch $BRANCH (\$GITHUB_BASE_REF $GITHUB_BASE_REF)"
+
+          git clone -b $BRANCH --depth 10 --single-branch https://github.com/easybuilders/easybuild-framework.git
+          cd easybuild-framework; git log -n 1; cd -
+          pip install $PWD/easybuild-framework
+
+          git clone -b $BRANCH --depth 10 --single-branch https://github.com/easybuilders/easybuild-easyblocks.git
+          cd easybuild-easyblocks; git log -n 1; cd -
+          pip install $PWD/easybuild-easyblocks
+
+    - name: install modules tool
+      run: |
+          cd $HOME
+          # use install_eb_dep.sh script provided with easybuild-framework
+          export INSTALL_DEP=$(which install_eb_dep.sh)
+          echo "Found install_eb_dep.sh script: $INSTALL_DEP"
+
+          # install modules tool
+          source $INSTALL_DEP ${{matrix.modules_tool}} $HOME
+
+          # changes in environment are not passed to other steps, so need to create files...
+          echo $MOD_INIT > mod_init
+          echo $PATH > path
+          if [ ! -z $MODULESHOME ]; then echo $MODULESHOME > moduleshome; fi
+
+    - name: run test suite
+      env:
+        EB_VERBOSE: 1
+        EASYBUILD_MODULE_SYNTAX: ${{matrix.module_syntax}}
+      run: |
+          # pull in target so we can diff against it to obtain list of touched files
+          if [ "x$GITHUB_BASE_REF" != 'xmain' ]; then git fetch -v origin ${GITHUB_BASE_REF}:${GITHUB_BASE_REF}; fi
+
+          # initialize environment for modules tool
+          if [ -f $HOME/moduleshome ]; then export MODULESHOME=$(cat $HOME/moduleshome); fi
+          source $(cat $HOME/mod_init); type module
+
+          # make sure 'eb' is available via $PATH, and that $PYTHONPATH is set (some tests expect that);
+          # also pick up changes to $PATH set by sourcing $MOD_INIT
+          WORKDIR=$GITHUB_WORKSPACE/easybuild-easyconfigs
+          export PATH=$WORKDIR/test/bin:$(cat $HOME/path)
+          export PYTHONPATH=$WORKDIR
+
+          # tell EasyBuild which modules tool is available
+          if [[ ${{matrix.modules_tool}} =~ ^modules-tcl- ]]; then
+            export EASYBUILD_MODULES_TOOL=EnvironmentModulesTcl
+          elif [[ ${{matrix.modules_tool}} =~ ^modules-3 ]]; then
+            export EASYBUILD_MODULES_TOOL=EnvironmentModulesC
+          elif [[ ${{matrix.modules_tool}} =~ ^modules-4 ]]; then
+            export EASYBUILD_MODULES_TOOL=EnvironmentModules
+          else
+            export EASYBUILD_MODULES_TOOL=Lmod
+          fi
+
+          eb --version
+          eb --show-config
+          # gather some useful info on test system
+          eb --show-system-info
+
+          # run test suite
+          # if tests failed, print error message that is picked up by boegelbot to determine end of test output
+          python -O -m test.easyconfigs.suite || (echo "ERROR: Not all tests were successful" && exit 1)
+
+          unset PYTHONPATH
+
+          # install easyconfigs via distribution package
+          python setup.py sdist > /dev/null
+          ls dist
+          pip install dist/easybuild-easyconfigs*tar.gz > /dev/null
+
+          # robot-paths value should not be empty, but have an entry that includes easybuild/easyconfigs subdir
+          echo "eb --show-config"
+          eb --show-config | tee eb_show_config.out
+          grep "^robot-paths .*/easybuild/easyconfigs" eb_show_config.out
+
+          # check whether some specific easyconfig files are found
+          echo "eb --search 'TensorFlow-1.14.*.eb'"
+          eb --search 'TensorFlow-1.14.*.eb' | tee eb_search_TF.out
+          grep '/TensorFlow-1.14.0-foss-2019a-Python-3.7.2.eb$' eb_search_TF.out
+
+          echo "eb --search '^foss-2019b.eb'"
+          eb --search '^foss-2019b.eb' | tee eb_search_foss.out
+          grep '/foss-2019b.eb$' eb_search_foss.out
+
+          # make sure CVS easyconfigs are included in installation (cfr. issue #10325)
+          echo "Searching for CVS easyconfigs..."
+          eb --search '^CVS-' | grep '/CVS-'
+
+          # try installing M4 with system toolchain (requires ConfigureMake easyblock + easyconfig)
+          # use /tmp/sources because that has cached downloads (see cache step above)
+          eb --prefix /tmp/$USER/$GITHUB_SHA --sourcepath /tmp/sources M4-1.4.18.eb
+
+  test-sdist:
+    runs-on: ubuntu-20.04
+    strategy:
+      matrix:
+        python: [2.7, 3.6, 3.7]
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: set up Python
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{matrix.python}}
+
+    - name: Create source distribution
+      run: python setup.py sdist
+
+    - name: Inspect files included in source distribution
+      working-directory: dist
+      run: |
+          tar xfz easybuild-easyconfigs*tar.gz
+          cd easybuild-easyconfigs-*/
+
+          # .git folder should not be there in source tarball
+          dot_git_files=$(find . -name .git)
+          if [ -n "$dot_git_files" ]; then
+            echo "Found .git folders in source tarball: $dot_git_files" && false
+          else
+            echo "No .git folders found in source tarball: OK"
+          fi
+
+          # CVS easyconfigs must be included in source tarball,
+          # see https://github.com/easybuilders/easybuild-easyconfigs/issues/10325
+          cvs_easyconfigs=$(find . -name 'CVS-*.eb')
+          if [ -z "$cvs_easyconfigs" ]; then
+            echo "CVS easyconfigs not found" && false
+          else
+            echo "Found CVS easyconfigs: $cvs_easyconfigs"
+          fi

.gitignore

@@ -10,3 +10,4 @@ dist/
 *.swp
 *.ropeproject/
 eb-*.log
+/MANIFEST

.pre-commit-config.yaml

@@ -0,0 +1,33 @@
+# To use these pre-commit hooks you should first install https://pre-commit.com
+# and then run "pre-commit install" in the root folder of your local clone
+# so the hooks are deployed to .git/hooks
+#
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+#
+# the pep8 custom config (e.g. custom line length) is defined in file .pep8
+# https://pep8.readthedocs.io/en/release-1.7.x/intro.html#configuration
+
+repos:
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    sha: v1.2.0
+    hooks:
+      - id: autopep8-wrapper
+        name: 'autopep8-wrapper (.eb)'
+        types: [file]
+        files: \.eb$
+      - id: check-ast
+        name: 'check-ast (.eb)'
+        types: [file]
+        files: \.eb$
+      - id: autopep8-wrapper
+      - id: check-ast
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-merge-conflict
+
+  - repo: https://github.com/easybuilders/pre-commit-hooks-easybuild
+    sha: v0.1
+    hooks:
+      - id: check-old-easybuild-url

CONTRIBUTING.md

@@ -5,7 +5,7 @@ We'd love you to contribute back to EasyBuild, and here's how you can do it: the
 
 ### Fork easybuild-easyconfigs
 
-First, you'll need to fork [easybuild-easyconfigs on GitHub](http://github.com/hpcugent/easybuild-easyconfigs).
+First, you'll need to fork [easybuild-easyconfigs on GitHub](https://github.com/easybuilders/easybuild-easyconfigs).
 
 If you do not have a (free) GitHub account yet, you'll need to get one.
 
@@ -25,10 +25,10 @@ Pull the _develop_ branch from the main easybuild-easyconfigs repository:
 
 ```bash
 cd easybuild
-git remote add github_hpcugent [email protected]:hpcugent/easybuild-easyconfigs.git
+git remote add github_easybuilders [email protected]:easybuilders/easybuild-easyconfigs.git
 git branch develop
 git checkout develop
-git pull github_hpcugent develop
+git pull github_easybuilders develop
 ```
 
 ### Keep develop up-to-date
@@ -39,7 +39,7 @@ Make sure you update it every time you create a feature branch (see below):
 
 ```bash
 git checkout develop
-git pull github_hpcugent develop
+git pull github_easybuilders develop
 ```
 
 
@@ -49,7 +49,7 @@ git pull github_hpcugent develop
 ### Pick a branch name
 
 Please try and follow these guidelines when picking a branch name:
- * use the number of the issue as a prefix for your branch name, e.g. `86_` for issue [#86](https://github.com/hpcugent/easybuild-framework/issues/86)
+ * use the number of the issue as a prefix for your branch name, e.g. `86_` for issue [#86](https://github.com/easybuilders/easybuild-framework/issues/86)
  * append a short but descriptive branch name, in which words are joined by underscores, e.g. `86_encoding_scheme`
 
 ### Create branch
@@ -113,7 +113,7 @@ If you're contributing code to an existing issue you can also convert the issue
 GITHUBUSER=your_username && PASSWD=your_password && BRANCH=branch_name && ISSUE=issue_number && \
 curl --user "$GITHUBUSER:$PASSWD" --request POST \
 --data "{\"issue\": \"$ISSUE\", \"head\": \"$GITHUBUSER:$BRANCH\", \"base\": \"develop\"}" \
-https://api.github.com/repos/hpcugent/easybuild-easyconfigs/pulls
+https://api.github.com/repos/easybuilders/easybuild-easyconfigs/pulls
 ```
 This is currently only supported by github from the command line and not via the web interface.
 You might also want to look into [hub](https://github.com/defunkt/hub) for more command line features.

MANIFEST.in

@@ -1,6 +1,4 @@
-recursive-include easybuild *
 include CONTRIBUTING.md
 include LICENSE
 include README.rst
 include RELEASE_NOTES
-include setup.py

README.rst

@@ -1,7 +1,9 @@
-.. image:: http://hpcugent.github.io/easybuild/images/easybuild_logo_small.png
+.. image:: https://github.com/easybuilders/easybuild-easyconfigs/workflows/easyconfigs%20unit%20tests/badge.svg
+
+.. image:: https://easybuilders.github.io/easybuild/images/easybuild_logo_small.png
    :align: center
 
-`EasyBuild <https://hpcugent.github.io/easybuild>`_ is a software build
+`EasyBuild <https://easybuilders.github.io/easybuild>`_ is a software build
 and installation framework that allows you to manage (scientific) software
 on High Performance Computing (HPC) systems in an efficient way.
 
@@ -15,31 +17,19 @@ The EasyBuild documentation is available at http://easybuild.readthedocs.org/.
 
 The easybuild-easyconfigs package is hosted on GitHub, along
 with an issue tracker for bug reports and feature requests, see
-http://github.com/hpcugent/easybuild-easyconfigs.
+https://github.com/easybuilders/easybuild-easyconfigs.
 
 Related Python packages:
 
 * **easybuild-framework**
 
   * the EasyBuild framework, which includes the ``easybuild.framework`` and ``easybuild.tools`` Python
     packages that provide general support for building and installing software
-  * GitHub repository: http://github.com/hpcugent/easybuild-framework
+  * GitHub repository: https://github.com/easybuilders/easybuild-framework
   * PyPi: https://pypi.python.org/pypi/easybuild-framework
 
 * **easybuild-easyblocks**
 
   * a collection of easyblocks that implement support for building and installing (groups of) software packages
-  * GitHub repository: http://github.com/hpcugent/easybuild-easyblocks
+  * GitHub repository: https://github.com/easybuilders/easybuild-easyblocks
   * package on PyPi: https://pypi.python.org/pypi/easybuild-easyblocks
-
-*Build status overview:*
-
-* **master** branch:
-
-  .. image:: https://travis-ci.org/hpcugent/easybuild-easyconfigs.svg?branch=master
-      :target: https://travis-ci.org/hpcugent/easybuild-easyconfigs/branches
-
-* **develop** branch:
-
-  .. image:: https://travis-ci.org/hpcugent/easybuild-easyconfigs.svg?branch=develop
-      :target: https://travis-ci.org/hpcugent/easybuild-easyconfigs/branches