Rework headers in docs etc. (#76)

* Rework headers in docs etc.

* fix gitignore

* Changes to qftrace, xpstrace, xrdtrace Usage.

* v110 of schemas

* Fix typos

* remove debug prints

* Version update

.github/workflows/docs-job/action.yml

@@ -3,7 +3,7 @@ description: "Build the documentation."
 runs:
   using: "composite"
   steps:
-    - run: sphinx-apidoc -o docs/source src/yadg -T -M
+    - run: sphinx-apidoc -o docs/source src/yadg -T -M -E -f --templatedir=docs/apidoc
       shell: bash
     - run: sphinx-build -W -b html docs/source public/master
       shell: bash

.gitignore

@@ -6,4 +6,5 @@ dist/
 *.egg-info
 *.egg
 build/
-public/
+public/
+docs/source/yadg*.rst

docs/apidoc/module.rst_t

@@ -0,0 +1,9 @@
+{%- if show_headings %}
+{{- [basename, "module"] | join(' ') | e | heading }}
+
+{% endif -%}
+.. automodule:: {{ qualname }}
+{%- for option in automodule_options %}
+   :{{ option }}:
+{%- endfor %}
+

docs/apidoc/package.rst_t

@@ -0,0 +1,79 @@
+{%- macro automodule(modname, options) -%}
+.. automodule:: {{ modname }}
+{%- for option in options %}
+   :{{ option }}:
+{%- endfor %}
+{%- endmacro %}
+
+{%- macro toctree(docnames) -%}
+.. toctree::
+   :maxdepth: {{ maxdepth }}
+{% for docname in docnames %}
+   {{ docname }}
+{%- endfor %}
+{%- endmacro %}
+
+{%- if is_namespace %}
+{{- [pkgname, "namespace"] | join(" ") | e | heading }}
+{% elif 'yadg.parsers.basiccsv' == pkgname %}
+{{- "**basiccsv**: Common tabular file parser" | heading }}
+{% elif 'yadg.parsers.chromdata' == pkgname %}
+{{- "**chromdata**: Post-processed chromatography data parser" | heading }}
+{% elif 'yadg.parsers.chromtrace' == pkgname %}
+{{- "**chromtrace**: Raw chromatogram trace file parser" | heading }}
+{% elif 'yadg.parsers.dummy' == pkgname %}
+{{- "**dummy**: A dummy parser" | heading }}
+{% elif 'yadg.parsers.electrochem' == pkgname %}
+{{- "**electrochem**: Electrochemistry data parser" | heading }}
+{% elif 'yadg.parsers.flowdata' == pkgname %}
+{{- "**flowdata**: Flow data parser" | heading }}
+{% elif 'yadg.parsers.masstrace' == pkgname %}
+{{- "**masstrace**: Mass spectroscopy trace file parser" | heading }}
+{% elif 'yadg.parsers.meascsv' == pkgname %}
+{{- "**meascsv**: Legacy MCPT log file parser" | heading }}
+{% elif 'yadg.parsers.qftrace' == pkgname %}
+{{- "**qftrace**: Network analyser trace file parser" | heading }}
+{% elif 'yadg.parsers.xpstrace' == pkgname %}
+{{- "**xpstrace**: XPS trace file parser" | heading }}
+{% elif 'yadg.parsers.xrdtrace' == pkgname %}
+{{- "**xrdtrace**: X-ray diffractogram trace file parser" | heading }}
+{% else %}
+{{- [pkgname, "package"] | join(" ") | e | heading }}
+{% endif %}
+
+{%- if is_namespace %}
+.. py:module:: {{ pkgname }}
+{% endif %}
+
+{%- if modulefirst and not is_namespace %}
+{{ automodule(pkgname, automodule_options) }}
+{% endif %}
+
+{%- if subpackages %}
+Subpackages
+-----------
+
+{{ toctree(subpackages) }}
+{% endif %}
+
+{%- if submodules %}
+Submodules
+----------
+{% if separatemodules %}
+{{ toctree(submodules) }}
+{% else %}
+{%- for submodule in submodules %}
+{% if show_headings %}
+{{- [submodule, "module"] | join(" ") | e | heading(2) }}
+{% endif %}
+{{ automodule(submodule, automodule_options) }}
+{% endfor %}
+{%- endif %}
+{%- endif %}
+
+{%- if not modulefirst and not is_namespace %}
+Module contents
+---------------
+
+{{ automodule(pkgname, automodule_options) }}
+{% endif %}

docs/source/_static/custom_theme.css

@@ -1,3 +1,6 @@
-.wy-nav-content {
+.wy-body-for-nav {
     max-width: none;
+}
+.wy-nav-content {
+    max-width: 1280px;
 }

docs/source/version.4_2.rst

@@ -15,20 +15,27 @@ Developed at Empa - Materials Science and Technology, in Dübendorf.
 
 New features since v4.1 are:
 
-  - :mod:`~yadg.parsers.chromdata` parser for parsing integrated chromatography data,
-
+  - :mod:`~yadg.parsers.chromdata` parser for parsing post-processed chromatography data.
 
-Bug fixes and other modifications include:
+Backwards-incompatible changes include:
 
-  - the ``drycal`` filetypes in :mod:`yadg.parsers.flowdata` should now work for 
-    overnight experiments;
   - the :mod:`~yadg.parsers.chromtrace` parser now focuses on parsing chromatography
-    traces only, with trace integration deprecated in favour of ``dgpost``;
+    traces only, use :mod:`~yadg.parsers.chromdata` for parsing post-processed chromatographic
+    data; 
   - the :mod:`~yadg.parsers.flowdata` parser now no longer creates a default ``"flow"``
-    entry in derived data;
-  - the ``calfile`` and ``calib`` parameters have been deprecated in favour of ``dgpost``;
+    entry in derived data;  
+  - data post-processing within :mod:`yadg`, including chromatographic trace integration,
+    reflection coefficient processing, and calibration functionality is deprecated in favour 
+    of ``dgpost``.
+
+Bug fixes include:
+
+  - the ``drycal`` filetypes in :mod:`~yadg.parsers.flowdata` should now work for 
+    overnight experiments;
   - the metadata in :mod:`~yadg.parsers.chromdata` and :mod:`~yadg.parsers.chromtrace`
     was modified to only include true metadata as opposed to sample data;
+  - the :mod:`~yadg.parsers.electrochem` parser now allows for toggling the transposing
+    of PEIS/GEIS traces.