Update changelog, license, requirements, docs (#5)

Author: rly

.gitignore

@@ -1,3 +1,7 @@
+# generated docs
+docs/source/_format_auto_docs
+
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

CHANGELOG.md

@@ -0,0 +1,9 @@
+# ndx-franklab-novela Changelog
+
+## 0.1.0 (December 9, 2021)
+
+- Removed `NdxImageSeries` data type. The core NWB `ImageSeries` type should be used instead.
+- Replaced all custom Python classes with autogenerated Python classes. This should not affect downstream code.
+- Updated authors, contact information, license, and readme.
+- Updated requirements to use the latest HDMF and PyNWB packages.
+- Added basic CI using GitHub Actions.

LICENSE.md

@@ -1,3 +1,18 @@
+Copyright 2021, NovelaNeurotechnologies, Loren Frank, Eric Denovellis, Ryan Ly
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
 Copyright 2020, NovelaNeurotechnologies
 
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
@@ -11,4 +26,4 @@ Redistribution and use in source and binary forms, with or without modification,
 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
 IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
 OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
-ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

docs/source/_static/theme_overrides.css

@@ -0,0 +1,13 @@
+/* override table width restrictions */
+@media screen and (min-width: 767px) {
+
+   .wy-table-responsive table td {
+      /* !important prevents the common CSS stylesheets from overriding
+         this as on RTD they are loaded after this stylesheet */
+      white-space: normal !important;
+   }
+
+   .wy-table-responsive {
+      overflow: visible !important;
+   }
+}

docs/source/conf.py

@@ -18,12 +18,12 @@
 # -- Project information -----------------------------------------------------
 
 project = 'ndx-franklab-novela'
-copyright = '2020, NovelaDevops'
-author = 'NovelaDevops'
+copyright = '2020-2021, NovelaNeurotechnologies, Loren Frank, Eric Denovellis, Ryan Ly'
+author = 'NovelaNeurotechnologies, Loren Frank, Eric Denovellis, Ryan Ly'
 
 # The short X.Y version
 
-version = '0.0.011.36'
+version = '0.1.0'
 
 
 # The full version, including alpha/beta/rc tags
@@ -49,7 +49,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = 'English'
+language = 'en'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -73,6 +73,12 @@
 # -- Extension configuration -------------------------------------------------
 
 # -- Options for intersphinx extension ---------------------------------------
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3', None),
+}
+
 ############################################################################
 #  CUSTOM CONFIGURATIONS ADDED BY THE NWB TOOL FOR GENERATING FORMAT DOCS
 ###########################################################################
@@ -81,7 +87,10 @@
 import textwrap  # noqa: E402
 
 # -- Options for intersphinx  ---------------------------------------------
-intersphinx_mapping = {'core': ('https://nwb-schema.readthedocs.io/en/latest/', None)}
+intersphinx_mapping.update({
+    'core': ('https://nwb-schema.readthedocs.io/en/latest/', None),
+    'hdmf-common': ('https://hdmf-common-schema.readthedocs.io/en/latest/', None),
+})
 
 # -- Generate sources from YAML---------------------------------------------------
 # Always rebuild the source docs from YAML even if the folder with the source files already exists
@@ -104,8 +113,11 @@ def run_doc_autogen(_):
 
 def setup(app):
     app.connect('builder-inited', run_doc_autogen)
-    app.add_stylesheet("theme_overrides.css")  # overrides for wide tables in RTD theme
-
+    # overrides for wide tables in RTD theme
+    try:
+        app.add_css_file("theme_overrides.css")  # Used by newer Sphinx versions
+    except AttributeError:
+        app.add_stylesheet("theme_overrides.css")  # Used by older version of Sphinx
 
 # -- Customize sphinx settings
 numfig = True

docs/source/conf_doc_autogen.py

@@ -6,7 +6,7 @@
 # -- Input options for the specification files to be used -----------------------
 
 # Directory where the YAML files for the namespace to be documented are located
-spec_input_spec_dir = '..\spec'
+spec_input_spec_dir = '../spec'
 
 # Name of the YAML file with the specification of the Namespace to be documented
 spec_input_namespace_filename = 'ndx-franklab-novela.namespace.yaml'

docs/source/index.rst

@@ -1,5 +1,5 @@
 Specification for the ndx-franklab-novela extension
-==================================
+===================================================
 
 .. toctree::
     :numbered:

environment.yml

@@ -7,6 +7,6 @@ dependencies:
   - python>=3.6
   - python-dateutil
   - setuptools
-  - hdmf
-  - pynwb
+  - hdmf>=3.1.1,<4
+  - pynwb>=2.0.0,<3
   - pytest

meta.yaml

@@ -12,15 +12,14 @@ build:
 
 requirements:
   build:
-    - python==3.6
+    - python==3.8
     - setuptools
-    - hdmf==1.6.4
+    - hdmf==3.1.1
     - python-dateutil
-    - pynwb==1.3.3
+    - pynwb==2.1.1
   run:
-    - python>=3.6,<3.7
+    - python>=3.6
     - python-dateutil
-    - hdmf==1.6.4
-    - pynwb==1.3.3
+    - hdmf==3.1.1,<4
+    - pynwb==2.0.0,<4
     - pytest
-