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‎.gitattributes‎

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*.nc filter=lfs diff=lfs merge=lfs -text

‎.gitignore‎

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doc/source/generated/
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**/__pycache__
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**/*.pyc
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doc/source/_static/*png
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doc/source/_static/movie.**
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**/compile.sh
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doc/_build
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doc/generated
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doc/_static/map*png
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doc/_static/temp*png
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doc/_static/*ogg

‎.vscode/settings.json‎

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{
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"esbonio.sphinx.confDir": "${workspaceFolder}/doc",
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"esbonio.sphinx.buildDir": "${confDir}/_build",
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}

‎.zenodo.json‎

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{
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"title": "Ichthyop Python package",
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"notes": "If you use this software, please cite it as below.",
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"creators": [
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{
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"name": "Barrier, Nicolas",
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"orcid": "0000-0002-1693-4719"
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},
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{
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"name": "Lett, Christophe",
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"orcid": "0000-0001-5809-2452"
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}
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],
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"communities": [
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{
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"identifier": "ichthyop"
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},
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{
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"identifier": "umr-marbec"
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}
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]
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}

‎CITATION.cff‎

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cff-version: 1.1.0
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message: "If you use this software, please cite it as below."
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authors:
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- family-names: Barrier
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given-names: Nicolas
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orcid: https://orcid.org/0000-0002-1693-4719
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- family-names: Lett
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given-names: Christophe
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orcid: https://orcid.org/0000-0001-5809-2452
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title: Ichthyop Python package
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version: 1.0.2
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date-released: 2023-02-28
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doi: 10.5281/zenodo.4109869

‎README.md‎

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Ichthyop (http://ichthyop.org/) is a free Java tool designed to study the effects of physical and biological factors on ichthyoplankton dynamics (code available [here](https://github.com/ichthyop/ichthyop)).
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This python package is dedicated to the analysis of Ichthyop's outputs.
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This python package is dedicated to the analysis of Ichthyop's outputs.
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- Plots trajectories (as a function of time, depth, etc.)
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- Make animations
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- Connectivity calculations

‎RELEASE.md‎

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# Release notes for Ichthyop python
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## Version 1.0.2
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### Bug fix
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- Correction in the use of the `cftime` library (no more `utime` variable)
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## Version 1.0.1
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### New features
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- Adding DOI badge
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## Version 1.0.0
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- First commit

‎doc/Makefile‎

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# Makefile for Sphinx documentation
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# Minimal 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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# You can set these variables from the command line, and also
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# from the environment for the first two.
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SPHINXOPTS ?=
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SPHINXBUILD ?= sphinx-build
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SOURCEDIR = .
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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) source
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# the i18n builder cannot share the environment and doctrees with the others
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I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
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.PHONY: help
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# Put it first so that "make" without argument is like "make 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 $(BUILDDIR)/*
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rm -rfv source/generated
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rm -rfv source/savefig
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.PHONY: html
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html:
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$(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/pyichthyop.qhcp"
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@echo "To view the help file:"
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@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/pyichthyop.qhc"
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.PHONY: applehelp
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applehelp:
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$(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 $$HOME/.local/share/devhelp/pyichthyop"
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@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/pyichthyop"
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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 $(BUILDDIR)/xml."
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@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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.PHONY: pseudoxml
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pseudoxml:
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$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
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@echo
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@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
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.PHONY: help Makefile
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.PHONY: dummy
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dummy:
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$(SPHINXBUILD) -b dummy $(ALLSPHINXOPTS) $(BUILDDIR)/dummy
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@echo
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@echo "Build finished. Dummy builder generates no files."
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# Catch-all target: route all unknown targets to Sphinx using the new
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# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
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%: Makefile
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@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

‎doc/_static/biblio.bib‎

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doc/source/examples/extract_date.py renamed to doc/_static/examples/extract_date.py

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import ichthyop.plot as ichplot
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import pylab as plt
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filename = 'source/_static/ichthyop-example.nc'
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filename = '_static/ichthyop-example.nc'
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#filename = '../_static/ichthyop-example.nc'
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# extracts the trajectories of drifters numbers with a step of 1000

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