Add core functionality for parsing attributes from an open file (#3)

.github/workflows/ci.yaml

@@ -66,6 +66,7 @@ jobs:
 
       - name: Install package
         run: |
+          sudo apt-get update && sudo apt-get install pandoc -y
           python -m pip install --upgrade pip
           python -m pip install -e .
 

.gitignore

@@ -102,3 +102,7 @@ venv.bak/
 
 # mypy
 .mypy_cache/
+
+
+.DS_Store
+.vscode/

.pre-commit-config.yaml

@@ -3,11 +3,11 @@ repos:
   -   repo: https://github.com/pre-commit/pre-commit-hooks
       rev: v2.5.0
       hooks:
-      -   id: trailing-whitespace
-      -   id: end-of-file-fixer
-      -   id: check-docstring-first
-      -   id: check-yaml
-      -   id: double-quote-string-fixer
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-docstring-first
+      - id: check-yaml
+      - id: double-quote-string-fixer
 
   -   repo: https://github.com/ambv/black
       rev: 19.10b0
@@ -24,8 +24,13 @@ repos:
   -   repo: https://github.com/asottile/seed-isort-config
       rev: v2.1.1
       hooks:
-      -   id: seed-isort-config
+      - id: seed-isort-config
   -   repo: https://github.com/pre-commit/mirrors-isort
       rev: v4.3.21
       hooks:
-      -   id: isort
+      - id: isort
+
+  -   repo: https://github.com/deathbeds/prenotebook
+      rev: master
+      hooks:
+       - id: prenotebook

CONTRIBUTING.rst

@@ -1,12 +1,12 @@
 =============================================
-Contributing to ecg
+Contributing to ecgtools
 =============================================
 
 Contributions are highly welcomed and appreciated.  Every little help counts,
 so do not hesitate!
 
 The following sections cover some general guidelines
-regarding development in ecg for maintainers and contributors.
+regarding development in ecgtools for maintainers and contributors.
 Nothing here is set in stone and can't be changed.
 Feel free to suggest improvements or changes in the workflow.
 
@@ -22,10 +22,10 @@ Feel free to suggest improvements or changes in the workflow.
 Feature requests and feedback
 -----------------------------
 
-Do you like ecg?  Share some love on Twitter or in your blog posts!
+Do you like ecgtools?  Share some love on Twitter or in your blog posts!
 
 We'd also like to hear about your propositions and suggestions.  Feel free to
-`submit them as issues <https://github.com/NCAR/ecg>`_ and:
+`submit them as issues <https://github.com/NCAR/ecgtools>`_ and:
 
 * Explain in detail how they should work.
 * Keep the scope as narrow as possible.  This will make it easier to implement.
@@ -36,13 +36,13 @@ We'd also like to hear about your propositions and suggestions.  Feel free to
 Report bugs
 -----------
 
-Report bugs for ecg in the `issue tracker <https://github.com/NCAR/ecg>`_.
+Report bugs for ecgtools in the `issue tracker <https://github.com/NCAR/ecgtools>`_.
 
 If you are reporting a bug, please include:
 
 * Your operating system name and version.
 * Any details about your local setup that might be helpful in troubleshooting,
-  specifically the Python interpreter version, installed libraries, and ecg
+  specifically the Python interpreter version, installed libraries, and ecgtools
   version.
 * Detailed steps to reproduce the bug.
 
@@ -56,15 +56,15 @@ fix the bug itself.
 Fix bugs
 --------
 
-Look through the `GitHub issues for bugs <https://github.com/NCAR/ecg/labels/type:%20bug>`_.
+Look through the `GitHub issues for bugs <https://github.com/NCAR/ecgtools/labels/type:%20bug>`_.
 
 Talk to developers to find out how you can fix specific bugs.
 
 
 Write documentation
 -------------------
 
-ecg could always use more documentation.  What exactly is needed?
+ecgtools could always use more documentation.  What exactly is needed?
 
 * More complementary documentation.  Have you perhaps found something unclear?
 * Docstrings.  There can never be too many of them.
@@ -93,21 +93,21 @@ Preparing Pull Requests
 
 
 #. Fork the
-   `ecg GitHub repository <https://github.com/NCAR/ecg>`__.  It's
-   fine to use ``ecg`` as your fork repository name because it will live
+   `ecgtools GitHub repository <https://github.com/NCAR/ecgtools>`__.  It's
+   fine to use ``ecgtools`` as your fork repository name because it will live
    under your user.
 
 #. Clone your fork locally using `git <https://git-scm.com/>`_ and create a branch::
 
-    $ git clone [email protected]:YOUR_GITHUB_USERNAME/ecg.git
-    $ cd ecg
+    $ git clone [email protected]:YOUR_GITHUB_USERNAME/ecgtools.git
+    $ cd ecgtools
     # now, to fix a bug or add feature create your own branch off "master":
 
     $ git checkout -b your-bugfix-feature-branch-name master
 
 
 
-#. Install `pre-commit <https://pre-commit.com>`_ and its hook on the ecg repo::
+#. Install `pre-commit <https://pre-commit.com>`_ and its hook on the ecgtools repo::
 
      $ pip install --user pre-commit
      $ pre-commit install
@@ -144,8 +144,8 @@ Preparing Pull Requests
 
 #. Finally, submit a pull request through the GitHub website using this data::
 
-    head-fork: YOUR_GITHUB_USERNAME/ecg
+    head-fork: YOUR_GITHUB_USERNAME/ecgtools
     compare: your-branch-name
 
-    base-fork: NCAR/ecg
+    base-fork: NCAR/ecgtools
     base: master

MANIFEST.in

@@ -1,6 +1,6 @@
 include LICENSE
 include README.rst
 
-recursive-include ecg *.py
+recursive-include ecgtools *.py
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]

README.rst

@@ -1,16 +1,16 @@
-.. image:: https://img.shields.io/github/workflow/status/NCAR/ecg/CI?logo=github&style=for-the-badge
-    :target: https://github.com/NCAR/ecg/actions
+.. image:: https://img.shields.io/github/workflow/status/NCAR/ecgtools/CI?logo=github&style=for-the-badge
+    :target: https://github.com/NCAR/ecgtools/actions
     :alt: GitHub Workflow CI Status
 
-.. image:: https://img.shields.io/github/workflow/status/NCAR/ecg/code-style?label=Code%20Style&style=for-the-badge
-    :target: https://github.com/NCAR/ecg/actions
+.. image:: https://img.shields.io/github/workflow/status/NCAR/ecgtools/code-style?label=Code%20Style&style=for-the-badge
+    :target: https://github.com/NCAR/ecgtools/actions
     :alt: GitHub Workflow Code Style Status
 
-.. image:: https://img.shields.io/codecov/c/github/NCAR/ecg.svg?style=for-the-badge
-    :target: https://codecov.io/gh/NCAR/ecg
+.. image:: https://img.shields.io/codecov/c/github/NCAR/ecgtools.svg?style=for-the-badge
+    :target: https://codecov.io/gh/NCAR/ecgtools
 
-ecg
-===
+ecgtools
+========
 
 Development
 ------------

ci/environment.yml

@@ -3,10 +3,12 @@ channels:
   - conda-forge
 dependencies:
   - codecov
+  - dask
+  - intake-esm
+  - nbsphinx
   - netcdf4
+  - numpydoc
   - pip
   - pytest
   - pytest-cov
   - xarray
-  - numpydoc
-  - nbsphinx

docs/requirements-docs.txt

@@ -1,4 +1,6 @@
-numpydoc
-sphinx-rtd-theme
+pydata-sphinx-theme
 nbsphinx
+ipykernel
 ipython
+pandoc
+-r ../requirements.txt

docs/source/api.rst

@@ -0,0 +1,16 @@
+.. currentmodule:: ecgtools
+
+#############
+API reference
+#############
+
+This is a reference API class listing, and modules.
+
+Builder Object
+===============
+
+.. autoclass:: Builder
+
+   .. automethod:: __init__
+   .. automethod:: parse_files_attributes
+   .. automethod:: create_catalog

docs/source/conf.py

@@ -15,7 +15,7 @@
 import os
 import sys
 
-import ecg
+import ecgtools
 
 # 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
@@ -41,15 +41,15 @@
     'sphinx.ext.doctest',
     'sphinx.ext.intersphinx',
     'sphinx.ext.extlinks',
-    'numpydoc',
+    'sphinx.ext.napoleon',
     'IPython.sphinxext.ipython_console_highlighting',
     'IPython.sphinxext.ipython_directive',
     'nbsphinx',
 ]
 
 extlinks = {
-    'issue': ('https://github.com/NCAR/ecg/issues/%s', 'GH#'),
-    'pr': ('https://github.com/NCAR/ecg/pull/%s', 'GH#'),
+    'issue': ('https://github.com/NCAR/ecgtools/issues/%s', 'GH#'),
+    'pr': ('https://github.com/NCAR/ecgtools/pull/%s', 'GH#'),
 }
 
 # Add any paths that contain templates here, relative to this directory.
@@ -60,33 +60,36 @@
 
 # Enable notebook execution
 # https://nbsphinx.readthedocs.io/en/0.4.2/never-execute.html
-# nbsphinx_execute = 'auto'
+nbsphinx_execute = 'auto'
 # Allow errors in all notebooks by
 nbsphinx_allow_errors = True
 
 # Disable cell timeout
 nbsphinx_timeout = -1
 
+autosummary_generate = []
 
+# Otherwise, the Return parameter list looks different from the Parameters list
+napoleon_use_rtype = False
 # The encoding of source files.
 # source_encoding = 'utf-8-sig'
 
 # The master toctree document.
 master_doc = 'index'
 
 # General information about the project.
-project = u'ecg'
+project = 'ecgtools'
 current_year = datetime.datetime.now().year
 copyright = f'2020-{current_year}, NCAR XDev Team'
-author = u'NCAR XDev Team'
+author = 'NCAR XDev Team'
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = ecg.__version__.split('+')[0]
+version = ecgtools.__version__.split('+')[0]
 # The full version, including alpha/beta/rc tags.
-release = ecg.__version__
+release = ecgtools.__version__
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -130,7 +133,7 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'sphinx_rtd_theme'
+html_theme = 'pydata_sphinx_theme'
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -203,7 +206,7 @@
 # html_file_suffix = None
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'ecgdoc'
+htmlhelp_basename = 'ecgtoolsdoc'
 
 
 # -- Options for LaTeX output --------------------------------------------------
@@ -220,7 +223,7 @@
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-    ('index', 'ecg.tex', u'ecg Documentation', u'NCAR XDev Team', 'manual'),
+    ('index', 'ecgtools.tex', 'ecgtools Documentation', 'NCAR XDev Team', 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -248,7 +251,7 @@
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [('index', 'ecg', u'ecg Documentation', [author], 1)]
+man_pages = [('index', 'ecgtools', 'ecgtools Documentation', [author], 1)]
 
 # If true, show URL addresses after external links.
 # man_show_urls = False
@@ -262,10 +265,10 @@
 texinfo_documents = [
     (
         'index',
-        'ecg',
-        u'ecg Documentation',
+        'ecgtools',
+        'ecgtools Documentation',
         author,
-        'ecg',
+        'ecgtools',
         'One line description of project.',
         'Miscellaneous',
     ),

docs/source/index.rst

@@ -7,11 +7,12 @@ Contents:
    :maxdepth: 2
 
    usage
+   api
 
 
 Feedback
 ========
 
 
-If you encounter any errors or problems with **ecg**,
-please open an issue at the GitHub http://github.com/NCAR/ecg main repository.
+If you encounter any errors or problems with **ecgtools**,
+please open an issue at the GitHub http://github.com/NCAR/ecgtools main repository.

docs/source/usage.rst

@@ -2,6 +2,6 @@
 Usage
 ========
 
-To use ecg in a project::
+To use ecgtools in a project::
 
-	import ecg
+	import ecgtools