From 9cfb3ccee39c43e9326b26647596ac3b15abc0f7 Mon Sep 17 00:00:00 2001
From: Joseph Hunkeler <jhunkeler@gmail.com>
Date: Mon, 4 Mar 2024 13:26:20 -0500
Subject: [PATCH 1/2] RTD integration begins

---
 .readthedocs.yml     |   4 ++++
 docs/Doxyfile        |  12 ++++++------
 docs/conf.py         |  43 +++++++++++++++++++++++++++++++++++++++++++
 docs/environment.yml |   8 ++++++++
 docs/index.rst       |   0
 docs/logo.png        | Bin 0 -> 10788 bytes
 6 files changed, 61 insertions(+), 6 deletions(-)
 create mode 100644 .readthedocs.yml
 create mode 100644 docs/conf.py
 create mode 100644 docs/environment.yml
 create mode 100644 docs/index.rst
 create mode 100644 docs/logo.png

diff --git a/.readthedocs.yml b/.readthedocs.yml
new file mode 100644
index 0000000..01c5cfa
--- /dev/null
+++ b/.readthedocs.yml
@@ -0,0 +1,4 @@
+version: 2
+
+conda:
+  environment: docs/environment.yml
diff --git a/docs/Doxyfile b/docs/Doxyfile
index d6509e6..05193d9 100644
--- a/docs/Doxyfile
+++ b/docs/Doxyfile
@@ -6,9 +6,9 @@
 DOXYFILE_ENCODING      = UTF-8
 PROJECT_NAME           = "Oh My Cal"
 PROJECT_NUMBER         =
-PROJECT_BRIEF          =
-PROJECT_LOGO           =
-OUTPUT_DIRECTORY       = docs/output
+PROJECT_BRIEF          = "A pipeline delivery generator"
+PROJECT_LOGO           = logo.png
+OUTPUT_DIRECTORY       =
 CREATE_SUBDIRS         = NO
 CREATE_SUBDIRS_LEVEL   = 8
 ALLOW_UNICODE_NAMES    = NO
@@ -124,7 +124,7 @@ WARN_LOGFILE           =
 #---------------------------------------------------------------------------
 # Configuration options related to the input files
 #---------------------------------------------------------------------------
-INPUT                  = README.md src include
+INPUT                  = ../README.md ../src ../include
 INPUT_ENCODING         = UTF-8
 INPUT_FILE_ENCODING    =
 FILE_PATTERNS          = *.c \
@@ -190,7 +190,7 @@ INPUT_FILTER           =
 FILTER_PATTERNS        =
 FILTER_SOURCE_FILES    = NO
 FILTER_SOURCE_PATTERNS =
-USE_MDFILE_AS_MAINPAGE = README.md
+USE_MDFILE_AS_MAINPAGE = ../README.md
 FORTRAN_COMMENT_AFTER  = 72
 #---------------------------------------------------------------------------
 # Configuration options related to source browsing
@@ -218,7 +218,7 @@ HTML_FILE_EXTENSION    = .html
 HTML_HEADER            =
 HTML_FOOTER            =
 HTML_STYLESHEET        =
-HTML_EXTRA_STYLESHEET  =
+HTML_EXTRA_STYLESHEET  = custom.css
 HTML_EXTRA_FILES       =
 HTML_COLORSTYLE        = AUTO_LIGHT
 HTML_COLORSTYLE_HUE    = 220
diff --git a/docs/conf.py b/docs/conf.py
new file mode 100644
index 0000000..e6b3cd6
--- /dev/null
+++ b/docs/conf.py
@@ -0,0 +1,43 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# 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.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+import os
+import shutil
+import subprocess
+
+print("current directory: {}".format(os.path.abspath(os.curdir)))
+if os.path.exists("html"):
+    shutil.rmtree("html")
+
+# Update doxygen config
+subprocess.run("doxygen -u", shell=True)
+
+# Run doxygen
+subprocess.run("doxygen", shell=True)
+
+# -- Project information -----------------------------------------------------
+
+project = 'Oh My Cal'
+copyright = '2023-2024, Space Telescope Science Institute'
+author = 'Joseph Hunkeler'
+
+html_extra_path = ["html"]
+
+# -- General configuration ---------------------------------------------------
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
diff --git a/docs/environment.yml b/docs/environment.yml
new file mode 100644
index 0000000..fed35ba
--- /dev/null
+++ b/docs/environment.yml
@@ -0,0 +1,8 @@
+name: RTD
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.11
+  - doxygen
+  - graphviz
diff --git a/docs/index.rst b/docs/index.rst
new file mode 100644
index 0000000..e69de29
diff --git a/docs/logo.png b/docs/logo.png
new file mode 100644
index 0000000000000000000000000000000000000000..c7f7ad5d14beb6a905624c95dcaff9841e630a9e
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From 5911c460a3a4d11dc42ea57e31caa66491f52819 Mon Sep 17 00:00:00 2001
From: Joseph Hunkeler <jhunkeler@gmail.com>
Date: Mon, 4 Mar 2024 13:37:58 -0500
Subject: [PATCH 2/2] RTD config

---
 .readthedocs.yml                           | 11 ++++++++++-
 docs/conf.py                               |  8 ++++++--
 docs/{environment.yml => environment.yaml} |  0
 docs/{index.rst => nop.rst}                |  0
 4 files changed, 16 insertions(+), 3 deletions(-)
 rename docs/{environment.yml => environment.yaml} (100%)
 rename docs/{index.rst => nop.rst} (100%)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 01c5cfa..aea6697 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -1,4 +1,13 @@
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: mambaforge-4.10
+
 conda:
-  environment: docs/environment.yml
+  environment: docs/environment.yaml
+
+sphinx:
+  configuration: docs/conf.py
+
diff --git a/docs/conf.py b/docs/conf.py
index e6b3cd6..6610bbd 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -16,23 +16,27 @@
 import os
 import shutil
 import subprocess
+import sys
+
+print("current directory: {}".format(os.path.abspath(os.curdir)), file=sys.stderr)
 
-print("current directory: {}".format(os.path.abspath(os.curdir)))
 if os.path.exists("html"):
     shutil.rmtree("html")
 
 # Update doxygen config
-subprocess.run("doxygen -u", shell=True)
+#subprocess.run("doxygen -u", shell=True)
 
 # Run doxygen
 subprocess.run("doxygen", shell=True)
 
+
 # -- Project information -----------------------------------------------------
 
 project = 'Oh My Cal'
 copyright = '2023-2024, Space Telescope Science Institute'
 author = 'Joseph Hunkeler'
 
+root_doc = "nop"
 html_extra_path = ["html"]
 
 # -- General configuration ---------------------------------------------------
diff --git a/docs/environment.yml b/docs/environment.yaml
similarity index 100%
rename from docs/environment.yml
rename to docs/environment.yaml
diff --git a/docs/index.rst b/docs/nop.rst
similarity index 100%
rename from docs/index.rst
rename to docs/nop.rst