Updated documentation and history for v1.3.1

This should also fix the Sphinx configuration so that RTD can import
ginput and include the autodocumented modules.

.gitignore

@@ -10,8 +10,7 @@
 .idea
 ginput/testing/plots/.*.pdf
 run_ginput.py
-# this will need to be unignored later
-^docs
+doc/build/**/*
 build/**/*
 dist/**/*
-.condaenv/**/*
+.condaenv/**/*

HISTORY.md

@@ -1,5 +1,12 @@
 # Ginput Version History
 
+## 1.3.1
+
+This release improves the ergonomics of including the time-varying O2 mole fraction
+by providing an option to the `O2MeanMoleFractionRecord` and a command line flag for
+the `vmr` and `rlvmr` subcommands to automatically download the necessary data and
+create/update the O2 mole fraction data file when creating `.vmr` files.
+
 ## 1.3.0
 
 This release primarily adds the ability to calculate a time-varying O2 mole fraction,

doc/source/conf.py

@@ -4,6 +4,9 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 import os
 import re
+import sys
+# Include the directory with ginput in it so autodoc finds the modules
+sys.path.insert(0, os.path.abspath('../..'))
 
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information

doc/source/ginput_usage/making_vmr_files.md

@@ -8,14 +8,6 @@ However, please note that GEOS FP is _not_ the standard met source for TCCON and
 ## Creating .vmr files for dates
 
 As with the previous steps, we will use the `run_ginput.py` script to call ginput.
-Before we can generate our `.vmr` files, we need to download one other set of input data, needed to calculate the global mean O2 mole fraction.
-To do this, simply run `./run_ginput.py update_fo2`; this will download the necessary data and write a file containing the mean O2 mole fractions calculated at `ginput/data/o2_mean_dmf.dat`.
-This command only needs run about once per year to update the data, but since it's pretty quick, running it more ofter (once a month or once a week even) is not a problem.
-
-```{note}
-The `update_fo2` subcommand was added in ginput v1.3.
-If you are using an older version of ginput, you will not have that subcommand, and ginput will not add the O2 mole fractions to the `.vmr` file headers.
-```
 
 To generate the actual `.vmr` files, we use the `vmr` subcommand.
 We'll assume that we are going to generate the `.vmr` files corresponding to the `.mod` files we made in {ref}`usage-mod`, so:
@@ -36,10 +28,18 @@ $ ./run_ginput.py vmr \
     --base-vmr-file ginput/testing/test_input_data/summer_35N.vmr \
     --integral-file ginput/testing/test_input_data/ap_51_level_0_to_70km.gnd \
     --save-path VMR_FILE_DIR \
+    --auto-update-fo2-file \
     20180101 \
     MOD_FILE_DIR/fp/xx/vertical
 ```
 
+```{note}
+ginput v1.3 added a requirement for O2 mole fraction data when generating the `.vmr` files.
+For v1.3, you would have to execute the command `./run_ginput update_fo2` once before creating any `.vmr` files.
+From v1.3.1 on, you can use the `--auto-update-fo2-file` flag for the `vmr` subcommand as shown below.
+If you are using a version of ginput before 1.3, you will not have the `update_fo2` subcommand nor the `--auto-update-fo2-file` flag, and ginput will not add the O2 mole fractions to the `.vmr` file headers.
+```
+
 This part of ginput requires several look up tables to be pre-calculated.
 The first time you run it, it will calculate them and save them as netCDF files.
 On successive runs, it will load the netCDF files unless any of the inputs or code needed to make those files have changed since the last run.
@@ -84,6 +84,7 @@ $ ./run_ginput.py rlvmr \
     --product fpit \
     --mod-root-dir MOD_FILE_DIR \
     --save-path VMR_FILE_DIR \
+    --auto-update-fo2-file \
     $gggpath/runlogs/gnd/pa_ggg_benchmark.grl
 ```
 

ginput/__init__.py

@@ -1,4 +1,4 @@
 # be sure to update in setup.py as well
 # and man/conf.py
 # please follow semantic versioning: https://semver.org/
-__version__ = '1.3.0'
+__version__ = '1.3.1'

install-dev-dependencies.sh

@@ -13,4 +13,10 @@ if [[ $? != 0 ]]; then
   echo "Warning: dot is not installed or not on your path. Some graphs in the documentation will not build. Please install graphviz with your package manager."
 fi
 
-conda install -c conda-forge sphinx sphinx_rtd_theme myst-parser linkify-it-py
+if [[ $GGG_USE_MICROMAMBA == "1" ]]; then
+  CMD=micromamba
+else
+  CMD=conda
+fi
+
+${CMD} install -c conda-forge sphinx sphinx_rtd_theme myst-parser linkify-it-py

man/source/conf.py

@@ -22,7 +22,7 @@
 author = 'Joshua Laughner, Sebastien Roche, and Matthaeus Kiel'
 
 # The full version, including alpha/beta/rc tags
-release = '1.3.0'
+release = '1.3.1'
 
 
 # -- General configuration ---------------------------------------------------
@@ -68,4 +68,3 @@
      [author], 1), 
     ('upnoaaman', 'ginput.upnoaa', 'Ginput: Update MLO/SMO monthly files', [author], 1)
 ]
-

setup.py

@@ -13,7 +13,7 @@
     long_description_content_type='text/markdown',
     author='Joshua Laughner, Sebastien Roche, Matthaeus Kiel',
     author_email='jlaugh@caltech.edu',
-    version='1.3.0',  # make sure stays in sync with the version in ginput/__init__.py
+    version='1.3.1',  # make sure stays in sync with the version in ginput/__init__.py
     url='',
     install_requires=[
         'astropy>=3.1.2',