Merge pull request #98 from cokelaer/main

refactor slurm/error modules

.github/workflows/main.yml

@@ -37,6 +37,7 @@ jobs:
     - name: install package itself
       run: |
          pip install poetry
+         pip install kaleido #required on github CI by plotly
          poetry install
 
     - name: testing

README.rst

@@ -288,6 +288,8 @@ Changelog
 ========= ======================================================================
 Version   Description
 ========= ======================================================================
+0.16.8    * stats command add the number of rules per pipeline
+          * better slurm parsing using profile tree directory (slurm in logs/)
 0.16.7    * add missing --trimming-quality option in list of TrimmingOption
           * set default to cutadatp if no fastp available
           * better UI for the completion script.

doc/conf.py

@@ -1,4 +1,4 @@
-# -*- coding: utf-8 -*-
+# . -*- coding: utf-8 -*-
 #
 # documentation build configuration file, created by
 # sphinx-quickstart on Wed Aug 10 16:58:13 2011.
@@ -11,67 +11,69 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys, os
+import os
+import sys
+
 import sphinx
 
-sys.path.insert(0, os.path.abspath('sphinxext'))
+sys.path.insert(0, os.path.abspath("sphinxext"))
 
 # 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.
 
 pkg_name = "sequana_pipetools"
 
-
-import pkg_resources
-version = pkg_resources.require(pkg_name)[0].version
+from sequana_pipetools import version
 
 release = version
 author = "Thomas Cokelaer"
 title = "sequana_pipetools"
 copyright = author + ", 2021"
-project = 'Sequana pipetools'
+project = "Sequana pipetools"
 
 
 # -- General configuration -----------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
+# needs_sphinx = '1.0'
 
 # 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.autodoc',
-    ('sphinx.ext.imgmath'  # only available for sphinx >= 1.4
-                  if sphinx.version_info[:2] >= (1, 4)
-                  else 'sphinx.ext.pngmath'),
-    'sphinx.ext.coverage',
-    'sphinx.ext.doctest',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.todo',
-    'sphinx.ext.ifconfig',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.autosummary',
-    ]
+    "sphinx.ext.autodoc",
+    (
+        "sphinx.ext.imgmath"  # only available for sphinx >= 1.4
+        if sphinx.version_info[:2] >= (1, 4)
+        else "sphinx.ext.pngmath"
+    ),
+    "sphinx.ext.coverage",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.autosummary",
+]
 # note that the numpy directives is buggy. Example: class and init are not recognised as two entities for the autoclass_content=both here below
 
 math_number_all = False
 
-todo_include_todos=True
-autoclass_content = 'both'
+todo_include_todos = True
+autoclass_content = "both"
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix of source filenames.
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The encoding of source files.
-#source_encoding = 'utf-8-sig'
+# source_encoding = 'utf-8-sig'
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
 project = project
@@ -82,34 +84,34 @@
 # built documents.
 #
 # The short X.Y version.
-version = 'Current version: ' + str(version) 
+version = "Current version: " + str(version)
 # The full version, including alpha/beta/rc tags.
 release = release
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
-#language = None
+# language = None
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
-#today = ''
+# today = ''
 # Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
+# today_fmt = '%B %d, %Y'
 
 # List of documents that shouldn't be included in the build.
-#unused_docs = []
+# unused_docs = []
 
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_trees = ['_build']
+exclude_trees = ["_build"]
 exclude_patterns = []
 
 # The reST default role (used for this markup: `text`) to use for all documents.
-#default_role = None
+# default_role = None
 
 # If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
+# add_function_parentheses = True
 
 # If true, the current module name will be prepended to all description
 # unit titles (such as .. function::).
@@ -120,14 +122,14 @@
 show_authors = True
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # A list of ignored prefixes for module index sorting.
 modindex_common_prefix = ["sequana_pipetools."]
 
 
 # for -- double dash to appear correctly
-smartquotes=False
+smartquotes = False
 
 # Get rid of spurious warnings due to some interaction between
 # autosummary and numpydoc. See
@@ -136,64 +138,61 @@
 numpydoc_show_class_members = False
 
 
-
-
-
 # -- Options for HTML output ---------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  Major themes that come with
 # Sphinx are currently 'default' and 'sphinxdoc'.
 import sphinx_rtd_theme
-html_theme = 'sphinx_rtd_theme'
+
+html_theme = "sphinx_rtd_theme"
 html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
 # the user theme contains the otpions 'homepage', which is populated here
-#html_theme_options = {'homepage': init_sphinx.url}
+# html_theme_options = {'homepage': init_sphinx.url}
 # Add any paths that contain custom themes here, relative to this directory.
 
 
-
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-#html_title = None
+# html_title = None
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
 html_short_title = "sequana"
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-#html_logo = "../../share/data/images/crx_logo.png"
+# html_logo = "../../share/data/images/crx_logo.png"
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-#html_favicon = "../../share/data/images/crx_logo.ico"
+# html_favicon = "../../share/data/images/crx_logo.ico"
 
 # 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']
+html_static_path = ["_static"]
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
-html_last_updated_fmt = '%b %d, %Y'
+html_last_updated_fmt = "%b %d, %Y"
 
 # If true, SmartyPants will be used to convert quotes and dashes to
 # typographically correct entities.
-#html_use_smartypants = True
+# html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-html_index = 'index.html'
+html_index = "index.html"
 
-#Custom sidebar templates, maps page names to templates.
-#html_sidebars = {
-#                    'index': [ 'indexsidebar.html'], 
+# Custom sidebar templates, maps page names to templates.
+# html_sidebars = {
+#                    'index': [ 'indexsidebar.html'],
 #                    'contents':'indexsidebar.html',
-#}
+# }
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
-#html_additional_pages = {   'index': 'index.html'}
+# html_additional_pages = {   'index': 'index.html'}
 
 
 # If false, no module index is generated.
@@ -213,18 +212,18 @@
 html_show_sphinx = True
 
 # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-#html_show_copyright = True
+# html_show_copyright = True
 
 # If true, an OpenSearch description file will be output, and all pages will
 # contain a <link> tag referring to it.  The value of this option must be the
 # base URL from which the finished HTML is served.
-#html_use_opensearch = ''
+# html_use_opensearch = ''
 
 # This is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = None
+# html_file_suffix = None
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'doc'
+htmlhelp_basename = "doc"
 
 
 # -- Options for LaTeX output --------------------------------------------------
@@ -233,52 +232,48 @@
 pngmath_use_preview = True
 
 # The font size ('10pt', '11pt' or '12pt').
-latex_font_size = '10pt'
+latex_font_size = "10pt"
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-  ('index', 'main.tex', title,
-   author, 'manual'),
+    ("index", "main.tex", title, author, "manual"),
 ]
 
-latex_elements = { 'inputenc': '\\usepackage[utf8]{inputenc}' }
+latex_elements = {"inputenc": "\\usepackage[utf8]{inputenc}"}
 
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
-#latex_logo = None
+# latex_logo = None
 
 # For "manual" documents, if this is true, then toplevel headings are parts,
 # not chapters.
 latex_use_parts = False
 
 # If true, show page references after internal links.
-#latex_show_pagerefs = False
+# latex_show_pagerefs = False
 
 # If true, show URL addresses after external links.
-#latex_show_urls = False
+# latex_show_urls = False
 
 # Additional stuff for the LaTeX preamble.
 
 
 # Documents to append as an appendix to all manuals.
-#latex_appendices = []
+# latex_appendices = []
 
 # If false, no module index is generated.
-#latex_domain_indices = True
+# latex_domain_indices = True
 
 
 # -- Options for manual page output --------------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    ('index', project, project,
-     [author], 1)
-]
+man_pages = [("index", project, project, [author], 1)]
 
 
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {
-    "python": ('http://docs.python.org/', None),
+    "python": ("http://docs.python.org/", None),
 }

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "poetry.core.masonry.api"
 #maintainer ?#maintainer email
 [tool.poetry]
 name = "sequana_pipetools"
-version = "0.16.7"
+version = "0.16.8"
 description = "A set of tools to help building or using Sequana pipelines"
 authors = ["Sequana Team"]
 license = "BSD-3"

sequana_pipetools/misc.py

@@ -13,7 +13,7 @@
 import hashlib
 import sys
 
-import pkg_resources
+from sequana_pipetools import get_package_version
 
 __all__ = ["Colors", "print_version", "error", "url2hash"]
 
@@ -88,21 +88,21 @@ def error(msg, pipeline):
 
 def print_version(name):
     try:
-        ver = pkg_resources.require("sequana_{}".format(name))[0].version
-        print("sequana_{} version: {}".format(name, ver))
+        ver = get_package_version(f"sequana_{name}")
+        print(f"sequana_{name} version: {ver}")
     except Exception as err:
         print(err)
-        print("sequana_{} version: ?".format(name))
+        print(f"sequana_{name} version: ?")
 
     try:
-        version = pkg_resources.require("sequana")[0].version
-        print("Sequana version: {}".format(version))
+        version = get_package_version(f"sequana")
+        print(f"Sequana version: {version}")
     except Exception:  # pragma: no cover
         pass
 
     try:
-        version = pkg_resources.require("sequana_pipetools")[0].version
-        print("Sequana_pipetools version: {}".format(version))
+        version = get_package_version(f"sequana_pipetools")
+        print(f"Sequana_pipetools version: {version}")
     except Exception as err:  # pragma: no cover
         print(err)
         print("Sequana_pipetools version: ?")