redid docs with newer version of sphinx - ready for release

Changelog.rst

@@ -1,6 +1,6 @@
 Changelog
 =========
 
-0.5.0 (2016-02-16)
+0.7.0 (2020-06-15)
 --------------------
-* xxxx
+* first release to pypi

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/*

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
@@ -69,70 +76,84 @@ 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
 ========================
 
 .. 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
 =================
 
 .. 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
 ============

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']