Readthedocs (#5)

* comment out pyre and journal in meta.yaml

* commented back

* fixed more typos

* commented out --no-deps

* formatting

* sectioning

---------

Co-authored-by: Patrou, Maria <patroum@ornl.gov>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Kyle Ma <maq1@ornl.gov>

.github/workflows/actions.yml

@@ -27,7 +27,7 @@ jobs:
     - name: pre-commit
       run: pre-commit run --all-files
     - name: Install histogram
-      run: python -m pip install -e . --no-deps
+      run: python -m pip install -e .
     - name: Run tests
       run: xvfb-run --server-args="-screen 0 1920x1080x24" -a python -m pytest --cov --cov-report=xml --cov-report=term --cov-config=.coveragerc
     - name: Upload coverage reports to Codecov

.readthedocs.yaml

@@ -0,0 +1,19 @@
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "mambaforge-4.10"
+
+python:
+  install:
+    - method: pip
+      path: .
+
+sphinx:
+  builder: html
+  configuration: docs/sphinx/conf.py
+  fail_on_warning: true
+
+conda:
+  environment: environment.yml

README.md

@@ -29,7 +29,7 @@ histogram data object
 
   .. code-block:: shell
 
-    $ pip install -e . --no-deps
+    $ pip install -e .
 
 * Tests
 

docs/sphinx/_static/default.css

@@ -21,7 +21,7 @@ body {
     margin: 0;
     /*min-width: 740px;*/
 
-    background-image:url('bg.png');
+    /* background-image:url('bg.png'); */
     background-repeat:no-repeat;
     background-position:bottom right;
     background-color:#777777;
@@ -170,7 +170,7 @@ div.document {
     /* opacity: 0.8;
     filter:alpha(opacity=80); */
     text-align: left;
-    background-image: url(contents.png);
+    /* background-image: url(contents.png); */
     background-repeat: repeat-x;
 }
 
@@ -195,7 +195,8 @@ div.related h3 {
 }
 
 div.related ul {
-    background-image: url(navigation.png);
+    /* background-image: url(navigation.png); */
+    background-color: black;
     height: 2em;
     list-style: none;
     border-top: 1px solid #ddd;
@@ -545,7 +546,7 @@ ul.search {
 
 ul.search li {
     padding: 5px 0 5px 20px;
-    background-image: url(file.png);
+    /* background-image: url(file.png); */
     background-repeat: no-repeat;
     background-position: 0 7px;
 }

docs/sphinx/_templates/layout.html

@@ -14,14 +14,14 @@
 <table><tr>
 <td>
 <div style="text-align: left; padding: 7px 7px 10px 10px">
-<a href="https://vnf.caltech.edu"><img class="logo" src="{{
-pathto("_static/logo.png", 1) }}" border="0" alt="py4sci"
+<a href="https://histogram-dev.readthedocs.io/en/latest/"><img class="logo" src="{{
+pathto("_static\logo.png", 1) }}" border="0" alt="py4sci"
   height="60"/></a>
 </div>
 </td>
 <td style="padding: 0pt 0pt 1em 3em;">
 <h1 class="title">
-histogram
+Histogram
 </h1>
 </td>
 </tr>

docs/sphinx/conf.py

@@ -30,7 +30,7 @@
     "sphinx.ext.intersphinx",
     "sphinx.ext.todo",
     "sphinx.ext.coverage",
-    "sphinx.ext.pngmath",
+    "sphinx.ext.imgmath",
     "sphinx.ext.ifconfig",
 ]
 
@@ -62,7 +62,7 @@
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
-# language = None
+language = "en"
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
@@ -130,6 +130,10 @@
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ["_static"]
 
+html_css_files = [
+    "default.css",
+]
+
 # 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'

docs/sphinx/install-details.rst

@@ -1,3 +1,5 @@
+:orphan:
+
 .. _install-details:
 
 Installation Details
@@ -19,13 +21,16 @@ Optionally, you may want to install:
 
 Install
 -------
-The histogram package can be installed by using easy_install::
+The histogram package can be installed by using pip install in editable mode currently::
+
+ $ git clone git@github.com:neutrons/histogram-dev.git.
+
+Navigate to the root directory of histogram-dev:::
 
- $ easy_install histogram
+ $ conda env create
 
-Or you can download histogram package from
-http://dev.danse.us/packages/histogram-0.2dev.tar.gz
+ (This will create an environment using the environment.yml file.)
 
-Expand and enter it, and run::
+To install the package, in the correct environment(histogram-dev)::
 
- $ python setup.py install
+ $ pip install -e .

docs/sphinx/install.rst

@@ -3,9 +3,16 @@
 Installation
 ============
 
-The histogram package can be installed by using easy_install::
+The histogram package can be installed by using pip install::
 
- $ easy_install histogram
+ Download the source code from https://github.com/neutrons/histogram-dev.
 
+ To install:
+
+ $ pip install -e .
+
+ To test, in the root directory type:
+
+ pytest
 
 :ref:`More details <install-details>`

docs/sphinx/intro.rst

@@ -40,7 +40,7 @@ Features
 * :ref:`Easy access to data as numpy arrays <I_E2>`
 * :ref:`Dump/load histograms in hdf format <save_load>`
 * :ref:`Quick plot using matplotlib <plot>`
-* Minimal GUI application that
+* :ref:`Minimal GUI application that is easy to use <gui>`
 
 
 Getting Started

docs/sphinx/python-interface.rst

@@ -88,8 +88,9 @@ some meta data, and two main datasets: "data" and "errors".
 
 * name: h.name()
 * bin centers of an axis: h.<axisname>
- - For example, a histogram has an axis named "x", then the bin
-   centers of "x" axis can be accessed as h.x.
+
+ - For example, a histogram has an axis named "x", then the bin centers of "x" axis can be accessed as h.x.
+
 * data (the "intensities" array): h.I
 * error squares (the squares of error bars array): h.E2
 
@@ -440,10 +441,16 @@ Save/load a histogram
 ^^^^^^^^^^^^^^^^^^^^^
 You can save/load a histogram in hdf5 format.
 
-* To save a histogram::
+* To save a histogram
+
+::
+
  >>> from histogram.hdf import dump
  >>> dump(h, 'myhist.h5')
 
-* To load a histogram::
+* To load a histogram
+
+::
+
  >>> from histogram.hdf import load
  >>> h = load('myhist.h5')

pyproject.toml

@@ -5,8 +5,6 @@ dynamic = ["version"]
 requires-python = ">=3.8"
 dependencies = [
   "numpy >= 1.20.3,< 2.0",
-  "pyre == 0.8.3",
-  "journal==0.8.4"
 ]
 license = { text = "MIT" }
 keywords = ["neutrons", "histogram", "python"]