diff --git a/Changelog.rst b/Changelog.rst index 3083277..9de524a 100644 --- a/Changelog.rst +++ b/Changelog.rst @@ -1,6 +1,6 @@ Changelog ========= -0.5.0 (2016-02-16) +0.7.0 (2020-06-15) -------------------- -* xxxx +* first release to pypi diff --git a/Makefile b/Makefile index e7873b0..0b73801 100644 --- a/Makefile +++ b/Makefile @@ -1,3 +1,22 @@ +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = . +BUILDDIR = docs/_build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + + all: build install .PHONY: build install test docs distclean dist upload @@ -12,9 +31,7 @@ test: pytest --verbose --disable-warnings --cov=pytaxize/ --ignore setup.py docs: - cd docs;\ - make html - # open _build/html/index.html + sphinx-build -b html docs/ docs/_build check: python3 -m twine check dist/* diff --git a/README.rst b/README.rst index 51e0337..dc46049 100644 --- a/README.rst +++ b/README.rst @@ -15,37 +15,44 @@ pytaxize is only developed in and tested with Python 3 Installation ============ +Stable from pypi + .. code-block:: console - sudo pip install git+git://github.com/sckott/pytaxize.git#egg=pytaxize + pip install pytaxize -python or ipython, etc. +Development version -.. code-block:: python +.. code-block:: console + + sudo pip install git+git://github.com/sckott/pytaxize.git#egg=pytaxize - import pytaxize Taxonomic Ids ============= I've started working on a class interface for taxonomic IDs, which will have a bunch of extension methods to do various things with taxon ids. What's available right now is just getting COL ids. -NOT WORKING YET! - .. code-block:: python - - res = pytaxize.Ids('Poa annua', db='col') - res.get_colid() + + from pytaxize import Ids + res = Ids('Poa annua') + res.ncbi() + res.ids .. code-block:: python - [19275187] + {'Poa annua': [{'id': '93036', + 'name': 'Poa annua', + 'rank': 'species', + 'uri': 'https://www.ncbi.nlm.nih.gov/taxonomy/93036'}]} Vascan search ============= .. code-block:: python - + + import pytaxize pytaxize.vascan_search(q = ["Helianthus annuus"]) .. code-block:: python @@ -69,21 +76,25 @@ Vascan search Scrape taxonomic names ====================== -NOT WORKING YET! - .. code-block:: python out = pytaxize.scrapenames(url = 'http://www.mapress.com/zootaxa/2012/f/z03372p265f.pdf') - out['data'].head() + out['data'][0:3] .. code-block:: python - identifiedName offsetEnd offsetStart scientificName verbatim - 0 Waxiella 14 7 Waxiella Waxiella - 1 W. africana 395 385 Waxiella africana W. africana - 2 W. egbara 581 573 Waxiella egbara W. egbara - 3 W. erithraeus 771 759 Waxiella erithraeus W. erithraeus - 4 W. gwaai 951 944 Waxiella gwaai W. gwaai + [{'verbatim': '(Hemiptera:', + 'scientificName': 'Hemiptera', + 'offsetStart': 222, + 'offsetEnd': 233}, + {'verbatim': 'Sternorrhyncha:', + 'scientificName': 'Sternorrhyncha', + 'offsetStart': 234, + 'offsetEnd': 249}, + {'verbatim': 'Coccoidea:', + 'scientificName': 'Coccoidea', + 'offsetStart': 250, + 'offsetEnd': 260}] ITIS low level functions ======================== @@ -91,28 +102,37 @@ ITIS low level functions .. code-block:: python from pytaxize import itis - itis.getacceptednamesfromtsn('208527') + itis.accepted_names(504239) - '208527' + {'acceptedName': 'Dasiphora fruticosa', + 'acceptedTsn': '836659', + 'author': '(L.) Rydb.'} .. code-block:: python - itis.getcommentdetailfromtsn(tsn=180543) + itis.comment_detail(tsn=180543) - comment \ - 0 Status: CITES - Appendix I as U. arctos (Mexic... - 1 Comments: Reviewed by Erdbrink (1953), Couturi... - - commentator commid commtime updatedate - 0 Wilson & Reeder, eds. (2005) 18556 2007-08-20 15:06:38.0 2014-02-03 - 1 Wilson & Reeder, eds. (2005) 18557 2007-08-20 15:06:38.0 2014-02-03 + [{'commentDetail': 'Status: CITES - Appendix I as U. arctos (Mexico, Bhutan, China, and Mongolia populations) and U. a. isabellinus; otherwise Appendix II. U. S. ESA - Endangered as U. arctos pruinosus, as U. arctos in Mexico, and as U. a. arctos in Italy. Threatened as U. a. ho...', + 'commentId': '18556', + 'commentTimeStamp': '2007-08-20 15:06:38.0', + 'commentator': 'Wilson & Reeder, eds. (2005)', + 'updateDate': '2014-02-03'}, + {'commentDetail': "Comments: Reviewed by Erdbrink (1953), Couturier (1954), Rausch (1963a), Kurtén (1973), Hall (1984) and Pasitschniak-Arts (1993). Ognev (1931) and Allen (1938) recognized U. pruinosus as distinct; not followed by Ellerman and Morrison-Scott (1951), Gao (1987), and Stroganov (1962). Lönnberg (1923b) believed that differences between pruinosus and arctos warranted subgeneric distinction as (Mylarctos) pruinosus; however, this was not supported by Pocock's (1932b) thorough revision. Synonyms allocated a...", + 'commentId': '18557', + 'commentTimeStamp': '2007-08-20 15:06:38.0', + 'commentator': 'Wilson & Reeder, eds. (2005)', + 'updateDate': '2014-02-03'}] .. code-block:: python - itis.gethierarchyupfromtsn(tsn = 36485) + itis.hierarchy_up(tsn = 36485) - author parentName parentTsn rankName taxonName tsn - 0 Raf. Asteraceae 35420 Genus Agoseris 36485 + {'author': 'Raf.', + 'parentName': 'Asteraceae', + 'parentTsn': '35420', + 'rankName': 'Genus', + 'taxonName': 'Agoseris', + 'tsn': '36485'} Catalogue of Life ================= @@ -120,19 +140,20 @@ Catalogue of Life .. code-block:: python from pytaxize import col - col.col_children(name=["Apis"]) - + x = col.children(name=["Apis"]) + x[0][0:3] .. code-block:: python - [ id name rank - 0 6971712 Apis andreniformis Species - 1 6971713 Apis cerana Species - 2 6971714 Apis dorsata Species - 3 6971715 Apis florea Species - 4 6971716 Apis koschevnikovi Species - 5 6845885 Apis mellifera Species - 6 6971717 Apis nigrocincta Species] + [{'id': '7a4a38c5095963949d6d6ec917d471de', + 'name': 'Apis andreniformis', + 'rank': 'Species'}, + {'id': '39610a4ceff7e5244e334a3fbc5e47e5', + 'name': 'Apis cerana', + 'rank': 'Species'}, + {'id': 'e1d4cbf3872c6c310b7a1c17ddd00ebc', + 'name': 'Apis dorsata', + 'rank': 'Species'}] Parse names =========== @@ -148,11 +169,20 @@ Parse names using GBIF's parser API .. code-block:: python - scientificName type genusOrAbove ... rankMarker - Arrhenatherum elatius var. elatius SCIENTIFIC Arrhenatherum ... var. - Secale cereale subsp. cereale SCIENTIFIC Secale ... subsp. - Secale cereale ssp. cereale SCIENTIFIC Secale ... subsp. - Vanessa atalanta (Linnaeus, 1758) SCIENTIFIC Vanessa ... sp. + [{'scientificName': 'Arrhenatherum elatius var. elatius', + 'type': 'SCIENTIFIC', + 'genusOrAbove': 'Arrhenatherum', + 'specificEpithet': 'elatius', + 'infraSpecificEpithet': 'elatius', + 'parsed': True, + 'parsedPartially': False, + 'canonicalName': 'Arrhenatherum elatius elatius', + 'canonicalNameWithMarker': 'Arrhenatherum elatius var. elatius', + 'canonicalNameComplete': 'Arrhenatherum elatius var. elatius', + 'rankMarker': 'var.'}, + {'scientificName': 'Secale cereale subsp. cereale', + 'type': 'SCIENTIFIC', + ... Contributors ============ diff --git a/conf.py b/conf.py new file mode 100644 index 0000000..e60d68b --- /dev/null +++ b/conf.py @@ -0,0 +1,55 @@ +# Configuration file for the Sphinx documentation builder. +# +# This file only contains a selection of the most common options. For a full +# list see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html + +# -- Path setup -------------------------------------------------------------- + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +# +# import os +# import sys +# sys.path.insert(0, os.path.abspath('.')) + + +# -- Project information ----------------------------------------------------- + +project = 'pytaxize' +copyright = '2020, Scott Chamberlain' +author = 'Scott Chamberlain' + + +# -- General configuration --------------------------------------------------- + +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom +# ones. +extensions = [ + 'sphinx.ext.intersphinx', + 'sphinx.ext.viewcode', + 'sphinx.ext.autodoc' +] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +# This pattern also affects html_static_path and html_extra_path. +exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] + + +# -- Options for HTML output ------------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +# +html_theme = 'sphinx_rtd_theme' + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ['_static'] diff --git a/docs/Makefile b/docs/Makefile deleted file mode 100644 index 53b56c7..0000000 --- a/docs/Makefile +++ /dev/null @@ -1,192 +0,0 @@ -# Makefile for Sphinx documentation -# - -# You can set these variables from the command line. -SPHINXOPTS = -SPHINXBUILD = sphinx-build -PAPER = -BUILDDIR = _build - -# User-friendly check for sphinx-build -ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) -$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/) -endif - -# Internal variables. -PAPEROPT_a4 = -D latex_paper_size=a4 -PAPEROPT_letter = -D latex_paper_size=letter -ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . -# the i18n builder cannot share the environment and doctrees with the others -I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . - -.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest coverage gettext - -help: - @echo "Please use \`make ' where is one of" - @echo " html to make standalone HTML files" - @echo " dirhtml to make HTML files named index.html in directories" - @echo " singlehtml to make a single large HTML file" - @echo " pickle to make pickle files" - @echo " json to make JSON files" - @echo " htmlhelp to make HTML files and a HTML help project" - @echo " qthelp to make HTML files and a qthelp project" - @echo " applehelp to make an Apple Help Book" - @echo " devhelp to make HTML files and a Devhelp project" - @echo " epub to make an epub" - @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" - @echo " latexpdf to make LaTeX files and run them through pdflatex" - @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx" - @echo " text to make text files" - @echo " man to make manual pages" - @echo " texinfo to make Texinfo files" - @echo " info to make Texinfo files and run them through makeinfo" - @echo " gettext to make PO message catalogs" - @echo " changes to make an overview of all changed/added/deprecated items" - @echo " xml to make Docutils-native XML files" - @echo " pseudoxml to make pseudoxml-XML files for display purposes" - @echo " linkcheck to check all external links for integrity" - @echo " doctest to run all doctests embedded in the documentation (if enabled)" - @echo " coverage to run coverage check of the documentation (if enabled)" - -clean: - rm -rf $(BUILDDIR)/* - -html: - $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html - @echo - @echo "Build finished. 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The XML files are in $(BUILDDIR)/xml." - -pseudoxml: - $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml - @echo - @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml." diff --git a/docs/_build/html/.buildinfo b/docs/_build/.buildinfo similarity index 82% rename from docs/_build/html/.buildinfo rename to docs/_build/.buildinfo index 52c44b7..9c51400 100644 --- a/docs/_build/html/.buildinfo +++ b/docs/_build/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. 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