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Merge pull request #7 from singularityhub/add/circle
adding circle testing
2 parents ec3e8fd + 4f49f37 commit a0bcc03

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‎.circleci/config.yml‎

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version: 2.1
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orbs:
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singularity: singularity/[email protected]
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################################################################################
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# Workflows
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################################################################################
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workflows:
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version: 2
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test:
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jobs:
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- run-scompose-ci-tests: &base_job
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filters:
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branches:
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ignore: master
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name: "Latest Singularity with Python 3"
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run-linter: true
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python: 3
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singularity: 3.2.1
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singularity-3: true
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################################################################################
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# Functions
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################################################################################
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run_linter: &run_linter
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name: run linter
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command: pylint ~/repo/scompose
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install_scompose: &install_scompose
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name: Install Singularity Compose
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command: |
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cd ~/repo
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pip install .[all]
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test_scompose: &test_scompose
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name: Test Singularity Compose
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command: |
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cd ~/repo
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pip install .[all]
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pytest scompose
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commands:
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install_dependencies:
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parameters:
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python:
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type: integer
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description: "Python version: 2 or 3"
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steps:
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- run: |
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PYTHON_VERSION="<< parameters.python >>"
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CONDA_PATH="$HOME/conda/Python${PYTHON_VERSION}"
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echo 'export PATH="'"$CONDA_PATH"'/bin:$PATH"' >> "$BASH_ENV"
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source "$BASH_ENV"
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if [ ! -d "$CONDA_PATH" ]; then
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CONDA_SCRIPT=Miniconda${PYTHON_VERSION}-latest-Linux-x86_64.sh
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wget https://repo.anaconda.com/miniconda/$CONDA_SCRIPT
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/bin/bash $CONDA_SCRIPT -b -p $CONDA_PATH
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else
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echo "Miniconda is already installed, continuing to build."
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fi
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python --version
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[ $(python -c'import sys;print(sys.version_info.major)') -eq $PYTHON_VERSION ]
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pip install --upgrade pylint pytest setuptools
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################################################################################
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# Jobs
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################################################################################
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jobs:
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run-scompose-ci-tests:
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parameters:
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run-linter:
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type: boolean
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default: false
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python:
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type: integer
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description: "Python version: 2 or 3"
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default: 3
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singularity:
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type: string
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description: "Singularity version"
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singularity-3:
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type: boolean
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description: "Set to true for singularity 3, false for singularity 2"
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default: true
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machine: true
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working_directory: ~/repo
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steps:
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- checkout
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- restore_cache:
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keys: v1-dependencies
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- install_dependencies:
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python: << parameters.python >>
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- when:
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condition: << parameters.singularity-3 >>
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steps:
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- singularity/install-go:
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go-version: 1.11.5
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- singularity/debian-install-3:
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singularity-version: << parameters.singularity >>
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- save_cache:
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paths:
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- ~/conda
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key: v1-dependencies
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- run: *install_scompose
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- when:
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condition: << parameters.run-linter >>
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steps:
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- run: *run_linter
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- run: *test_scompose

‎.docs/Makefile‎

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# Makefile for Sphinx documentation
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#
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# You can set these variables from the command line.
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SPHINXOPTS =
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SPHINXBUILD = sphinx-build
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PAPER =
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BUILDDIR = _build
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# Internal variables.
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PAPEROPT_a4 = -D latex_paper_size=a4
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PAPEROPT_letter = -D latex_paper_size=letter
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ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
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# the i18n builder cannot share the environment and doctrees with the others
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I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
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.PHONY: help
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help:
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@echo "Please use \`make <target>' where <target> is one of"
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@echo " html to make standalone HTML files"
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@echo " dirhtml to make HTML files named index.html in directories"
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@echo " singlehtml to make a single large HTML file"
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@echo " pickle to make pickle files"
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@echo " json to make JSON files"
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@echo " htmlhelp to make HTML files and a HTML help project"
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@echo " qthelp to make HTML files and a qthelp project"
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@echo " applehelp to make an Apple Help Book"
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@echo " devhelp to make HTML files and a Devhelp project"
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@echo " epub to make an epub"
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@echo " epub3 to make an epub3"
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@echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
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@echo " latexpdf to make LaTeX files and run them through pdflatex"
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@echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
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@echo " text to make text files"
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@echo " man to make manual pages"
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@echo " texinfo to make Texinfo files"
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@echo " info to make Texinfo files and run them through makeinfo"
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@echo " gettext to make PO message catalogs"
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@echo " changes to make an overview of all changed/added/deprecated items"
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@echo " xml to make Docutils-native XML files"
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@echo " pseudoxml to make pseudoxml-XML files for display purposes"
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@echo " linkcheck to check all external links for integrity"
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@echo " doctest to run all doctests embedded in the documentation (if enabled)"
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@echo " coverage to run coverage check of the documentation (if enabled)"
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@echo " dummy to check syntax errors of document sources"
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.PHONY: clean
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clean:
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rm -rf $(BUILDDIR)/*
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.PHONY: html
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html:
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$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
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@echo
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@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
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.PHONY: dirhtml
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dirhtml:
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$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
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@echo
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@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
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.PHONY: singlehtml
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singlehtml:
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$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
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@echo
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@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
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.PHONY: pickle
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pickle:
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$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
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@echo
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@echo "Build finished; now you can process the pickle files."
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.PHONY: json
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json:
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$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
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@echo
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@echo "Build finished; now you can process the JSON files."
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.PHONY: htmlhelp
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htmlhelp:
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$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
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@echo
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@echo "Build finished; now you can run HTML Help Workshop with the" \
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".hhp project file in $(BUILDDIR)/htmlhelp."
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.PHONY: qthelp
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qthelp:
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$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
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@echo
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@echo "Build finished; now you can run "qcollectiongenerator" with the" \
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".qhcp project file in $(BUILDDIR)/qthelp, like this:"
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@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/SingularityPythonAPI.qhcp"
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@echo "To view the help file:"
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@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/SingularityPythonAPI.qhc"
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.PHONY: applehelp
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applehelp:
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$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
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@echo
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@echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
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@echo "N.B. You won't be able to view it unless you put it in" \
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"~/Library/Documentation/Help or install it in your application" \
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"bundle."
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.PHONY: devhelp
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devhelp:
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$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
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@echo
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@echo "Build finished."
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@echo "To view the help file:"
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@echo "# mkdir -p $$HOME/.local/share/devhelp/SingularityPythonAPI"
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@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/SingularityPythonAPI"
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@echo "# devhelp"
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.PHONY: epub
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epub:
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$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
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@echo
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@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
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.PHONY: epub3
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epub3:
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$(SPHINXBUILD) -b epub3 $(ALLSPHINXOPTS) $(BUILDDIR)/epub3
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@echo
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@echo "Build finished. The epub3 file is in $(BUILDDIR)/epub3."
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.PHONY: latex
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latex:
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$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
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@echo
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@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
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@echo "Run \`make' in that directory to run these through (pdf)latex" \
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"(use \`make latexpdf' here to do that automatically)."
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.PHONY: latexpdf
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latexpdf:
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$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
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@echo "Running LaTeX files through pdflatex..."
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$(MAKE) -C $(BUILDDIR)/latex all-pdf
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@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
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.PHONY: latexpdfja
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latexpdfja:
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$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
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@echo "Running LaTeX files through platex and dvipdfmx..."
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$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
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@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
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.PHONY: text
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text:
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$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
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@echo
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@echo "Build finished. The text files are in $(BUILDDIR)/text."
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.PHONY: man
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man:
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$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
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@echo
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@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
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.PHONY: texinfo
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texinfo:
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$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
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@echo
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@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
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@echo "Run \`make' in that directory to run these through makeinfo" \
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"(use \`make info' here to do that automatically)."
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.PHONY: info
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info:
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$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
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@echo "Running Texinfo files through makeinfo..."
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make -C $(BUILDDIR)/texinfo info
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@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
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.PHONY: gettext
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gettext:
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$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
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@echo
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@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
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.PHONY: changes
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changes:
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$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
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@echo
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@echo "The overview file is in $(BUILDDIR)/changes."
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.PHONY: linkcheck
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linkcheck:
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$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
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@echo
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@echo "Link check complete; look for any errors in the above output " \
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"or in $(BUILDDIR)/linkcheck/output.txt."
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.PHONY: doctest
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doctest:
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$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
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@echo "Testing of doctests in the sources finished, look at the " \
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"results in $(BUILDDIR)/doctest/output.txt."
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.PHONY: coverage
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coverage:
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$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
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@echo "Testing of coverage in the sources finished, look at the " \
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"results in $(BUILDDIR)/coverage/python.txt."
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.PHONY: xml
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xml:
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$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
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@echo
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@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
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.PHONY: pseudoxml
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pseudoxml:
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$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
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@echo
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@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
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.PHONY: dummy
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dummy:
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$(SPHINXBUILD) -b dummy $(ALLSPHINXOPTS) $(BUILDDIR)/dummy
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@echo
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@echo "Build finished. Dummy builder generates no files."

‎.docs/apidoc.sh‎

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#!/bin/bash
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# If the modules changed, the content of "source" should be backed up and
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# new files generated (to update) by doing:
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#
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# sphinx-apidoc -o source/ ../scompose
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HERE="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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BASE=$(dirname $HERE)
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cd $HERE
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cd $BASE && python setup.py install && cd $HERE && make html
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rm -rf $BASE/docs/api
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# Create new folders
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mkdir -p $BASE/docs/api
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# Rename folders
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find $HERE/_build/html -exec sed -i -e 's/_static/assets/g' {} \;
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find $HERE/_build/html -exec sed -i -e 's/_modules/modules/g' {} \;
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# Copy to new locations
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mv $HERE/_build/html/_static $BASE/docs/api/assets
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mv $HERE/_build/html/_modules $BASE/docs/api/modules
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cp -R $HERE/_build/html/* $BASE/docs/api

‎.docs/changelog.md‎

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../CHANGELOG.md

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