Delete all requirements txt files and update documentation accordingly

CHANGELOG.rst

@@ -6,6 +6,7 @@ Version 3.0.2
 - Fix 'raw' mode in ``neurom stats``.
 - Add example astrocyte analysis notebook.
 - Fix readthedocs documentation build.
+- Delete all requirements txt files and update documentation accordingly
 
 Version 3.0.1
 -------------

doc/source/conf.py

@@ -53,35 +53,21 @@
 
 # -- General configuration ------------------------------------------------
 
-# If your documentation needs a minimal Sphinx version, state it here.
-needs_sphinx = '1.1'
-
 # 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_autorun',
     'sphinx.ext.autodoc',
     'sphinx.ext.autosummary',
-    'sphinx.ext.todo',
-    'sphinx.ext.viewcode',
     'sphinx.ext.napoleon',
 ]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
-# The suffix(es) of source filenames.
-# You can specify multiple suffix as a list of string:
-# source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
-
 # The encoding of source files.
 #source_encoding = 'utf-8-sig'
 
-# The master toctree document.
-master_doc = 'index'
-
 # General information about the project.
 project = u'NeuroM'
 author = u'BBP Algorithm Development Section'
@@ -127,25 +113,17 @@
 # output. They are ignored by default.
 #show_authors = False
 
-# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
-
 # A list of ignored prefixes for module index sorting.
 #modindex_common_prefix = []
 
 # If true, keep warnings as "system message" paragraphs in the built documents.
 #keep_warnings = False
 
-# If true, `todo` and `todoList` produce output, else they produce nothing.
-todo_include_todos = True
 suppress_warnings = ["ref.python"]
 autosummary_generate = True
-autosummary_imported_members = False
 autoclass_content = 'both'
 autodoc_default_options = {
     'members': True,
-    'imported-members': False,
-    'show-inheritance': True,
 }
 autosummary_mock_imports = ['plotly']
 
@@ -165,8 +143,6 @@
     "repo_name": "BlueBrain/NeuroM"
 }
 
-# Add any paths that contain custom themes here, relative to this directory.
-html_theme_path = ['_themes']
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
@@ -249,33 +225,8 @@
 # implements a search results scorer. If empty, the default will be used.
 #html_search_scorer = 'scorer.js'
 
-# Output file base name for HTML help builder.
-htmlhelp_basename = 'NeuroMdoc'
-
 # -- Options for LaTeX output ---------------------------------------------
 
-latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-#'papersize': 'letterpaper',
-
-# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
-
-# Additional stuff for the LaTeX preamble.
-#'preamble': '',
-
-# Latex figure (float) alignment
-#'figure_align': 'htbp',
-}
-
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title,
-#  author, documentclass [howto, manual, or own class]).
-latex_documents = [
-  (master_doc, 'NeuroM.tex', u'NeuroM Documentation',
-   u'HBP Algorithm Development Section', 'manual'),
-]
-
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
 #latex_logo = None
@@ -299,27 +250,10 @@
 
 # -- Options for manual page output ---------------------------------------
 
-# One entry per manual page. List of tuples
-# (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'neurom', u'NeuroM Documentation',
-     [author], 1)
-]
-
 # If true, show URL addresses after external links.
 #man_show_urls = False
 
 
-# -- Options for Texinfo output -------------------------------------------
-
-# Grouping the document tree into Texinfo files. List of tuples
-# (source start file, target name, title, author,
-#  dir menu entry, description, category)
-texinfo_documents = [
-  (master_doc, 'NeuroM', u'NeuroM Documentation',
-   author, 'NeuroM', 'One line description of project.',
-   'Miscellaneous'),
-]
 
 # Documents to append as an appendix to all manuals.
 #texinfo_appendices = []
@@ -329,30 +263,3 @@
 
 # How to display URL addresses: 'footnote', 'no', or 'inline'.
 #texinfo_show_urls = 'footnote'
-
-# If true, do not generate a @detailmenu in the "Top" node's menu.
-#texinfo_no_detailmenu = False
-from sphinx.ext.autosummary import Autosummary
-
-class AutosummaryOverride(Autosummary):
-    """Extends Autosummary to ensure the nosignatures option is set."""
-
-    def run(self):
-        """Wrap the autodoc output in a div with autodoc class."""
-        self.options["nosignatures"] = self.options.get("nosignatures", True)
-        result = super(AutosummaryOverride, self).run()
-        return result
-
-def add_autosummary_override(app):
-    """Override the autosummary definition to ensure no signatures."""
-    if "sphinx.ext.autosummary" in app.extensions:
-        app.add_directive("autosummary", AutosummaryOverride, override=True)
-
-def allow_only_neurom(app, what, name, obj, skip, options):
-    """Check that the member is part of neurom, exlude otherwise."""
-    if what in {"module", "class", "exception", "function"} and "neurom" not in getattr(obj, "__module__", ""):
-        return True
-
-def setup(app):
-    app.connect('builder-inited', add_autosummary_override)
-    app.connect('autodoc-skip-member', allow_only_neurom)

doc/source/developer.rst

@@ -45,58 +45,36 @@ Running the tests
 -----------------
 
 The tests require that you have cloned the repository, since the test code is
-not distributed in the package. It is recommended to use ``pytest`` for
-this. There are two options:
-
-Use the provided ``Makefile`` to run the tests using ``make``:
+not distributed in the package. It is recommended to use ``tox`` for this.
 
 .. code-block:: bash
 
     $ git clone https://github.com/BlueBrain/NeuroM.git
     $ cd NeuroM
-    $ make test
-
-This runs ``pep8``, ``pylint`` and the unit tests in sequence.
+    $ tox
 
-This method takes care of
-installing all extra dependencies needed for running the tests, diagnosing the results,
-performing linting on the source code. These dependencies are installed into a
-``virtuanelv`` named ``neurom_test_venv``:
-
-The ``Makefile`` also has targets for running only ``pylint`` and ``pep8`` individually:
+This method takes care of installing all extra dependencies needed for tests, diagnosing results,
+etc. It runs documentation check, pylint and the tests in sequence. Also it can run them
+individually:
 
 .. code-block:: bash
 
-        $ make lint       # runs pep8 and pylint if that succeeds
-        $ make run_pep8   # run only pep8
-        $ make run_pylint # run only pylint
-
+        $ tox -e py36-lint       # runs only pylint
+        $ tox -e py36-docs       # run only documentation check
+        $ tox -e py36            # run only the tests
 
-Note that you can also install the test dependencies and run the tests inside of your
-own ``virtualenv``:
+You can also run tests manually via `pylint` but you need to make sure that you have installed
+all required dependencies in your virtual environment:
 
 .. code-block:: bash
 
-    (nrm)$ pip install -r requirements_dev.txt
+    (your virtual env name)$ pip install neurom[plotly] pytest mock
 
-This installs the following packages into your ``virtualenv``
-unless they are already installed:
-
-.. literalinclude:: ../../requirements_dev.txt
-    :lines: 29-36
-
-Then, run the tests manually in the ``virtualenv``. For example,
+Then, run the tests manually. For example,
 
 .. code-block:: bash
 
-    (nrm)$ pytest --cov-report term-missing --cov-report xml --cov-report html --cov=neurom neurom
-
-.. warning::
-
-    To ensure that the test requirements are the same as those run in continuous
-    integration, you should run the tests using the ``make test`` command. This is the
-    same command used in continuous integration. Failure to pass means will result in
-    a pull request being rejected.
+    (your virtual env name)$ pytest tests
 
 .. include:: documentation.rst
 

doc/source/documentation.rst

@@ -35,8 +35,8 @@ To build documentation, go into project's ``doc`` folder.
 
     $ cd doc  # assuming that you start from the project's root.
 
-Make sure you have installed into your virtual environment libraries from ``requirements_docs.txt``
-in the project's root. Run the command:
+Make sure you have installed into your virtual environment libraries from `docs` extras:
+``pip install neurom[docs]``. Then run the command in the ``doc`` folder:
 
 .. code-block:: bash
 

neurom/core/types.py

@@ -117,6 +117,7 @@ def check_tree_type(tree):
 
 def dendrite_filter(n):
     """Select only dendrites."""
+    # pylint: disable=consider-using-in
     return n.type == NeuriteType.basal_dendrite or n.type == NeuriteType.apical_dendrite
 
 

pylintrc

@@ -6,7 +6,7 @@
 #R0903 - Too Few public methods
 #W0511 - TODO in code
 #R0401 - cyclic-import
-disable=C0103,R0903,W0511,R0401,unspecified-encoding
+disable=C0103,R0903,W0511,R0401,unspecified-encoding,consider-using-f-string
 
 [FORMAT]
 # Maximum number of characters on a single line.

setup.py

@@ -53,8 +53,8 @@
     },
     name='neurom',
     extras_require={
-        'plotly': ['plotly>=3.6.0',
-                   'psutil>=5.5.1'],  # for plotly image saving
+        'plotly': ['plotly>=3.6.0', 'psutil>=5.5.1'],  # for plotly image saving
+        'docs': ['sphinx', 'sphinx-bluebrain-theme', 'sphinx-autorun'],
     },
     include_package_data=True,
     python_requires='>=3.5',

tox.ini

@@ -40,7 +40,7 @@ commands =
 
 [testenv:py36-docs]
 changedir = doc
-deps = -r requirements_docs.txt
+extras = docs
 commands =
     # remove autosummary output
     rm -rf {toxinidir}/doc/source/_neurom_build