Merge pull request #222 from ESGF/bugfix_version_yaml

update to fix
ESGF · Sep 19, 2023 · 15f3a89 · 15f3a89
2 parents c0aa590 + c54244f
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diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,22 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# We recommend specifying your dependencies to enable reproducible builds:
+# https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+# python:
+#   install:
+#   - requirements: docs/requirements.txt
diff --git a/README.md b/README.md
@@ -1,11 +1,14 @@
 # ESGF Publisher
 
-`v5.2.0` is the latest release of the ESGF Publisher.  We recommend everyone to upgrade to this version.
+`v5.2.1` is the latest release of the ESGF Publisher.  We recommend everyone to upgrade to this version.
 
-See: https://esg-publisher.readthedocs.io/en/latest
+See: https://esg-publisher.readthedocs.io/
 
 ### Release notes:
 
+#### v5.2.1
+* **BUGFIX**:  Missing `import` caused ``esgpublish`` calls to fail in most cases.
+
 #### v5.2.0 - Major release
 * Migrated configuration from `.ini` format to `.yaml`.  Use `esgmigrate` to convert existing `.ini` files.
 *  Added XArray for NetCDF file reading.  Disable autocurator in settings to use or add `--xarray`

diff --git a/docs/cmor.rst b/docs/cmor.rst
@@ -2,12 +2,14 @@ CMOR
 ====
 
 Before running the publisher for CMIP6, you will need to obtain a directory of CMOR tables, used by PrePARE to check the metadata of your files.
-You can get this directory either using ``esgprep`` or by cloning the git repository.
+You can get this directory either using ``esgprep`` or by cloning the git repository.  CMOR/PrePARE is available for Linux and MacOS Intel.  Mac Apple M1 systems are not currently supported.
+
+NOTE: ``esgprep`` uses python 2.6 or greater, but less than python 3.0. Configure your virtual environment as needed.
 
 esgprep
 -------
 
-You can install ``esgprep`` using pip::
+You can install ``esgprep`` (esgf-prepare) using pip::
 
     pip install esgprep
 
@@ -17,8 +19,6 @@ You can also clone their git repository and run setup.py::
     cd esgf-prepare
     python setup.py install
 
-NOTE: ``esgprep`` uses python 2.6 or greater, but less than python 3.0. Configure your virtual environment as needed.
-
 Following install, simply run::
 
     esgfetchtables
@@ -28,6 +28,7 @@ You can specify project using ``--project`` and the output directory using ``--t
     esgfetchtables --project CMIP6 --table-dir <path>
 
 Once you have fetched the tables, you can update the ``cmor_path`` variable in your config file, or specify it at run time in the command line.
+See https://esgf.github.io/esgf-prepare/ for more information.
 
 Clone Git Repository
 --------------------

diff --git a/docs/conf.py b/docs/conf.py
@@ -13,7 +13,7 @@
 # import os
 # import sys
 # sys.path.insert(0, os.path.abspath('.'))
-import sphinx_glpi_theme
+import sphinx_rtd_theme
 
 # -- Project information -----------------------------------------------------
 
@@ -22,7 +22,7 @@
 author = 'Elysia Witham, Sasha Ames'
 
 # The full version, including alpha/beta/rc tags
-release = '5.1.0b11'
+release = '5.2.1'
 
 
 # -- General configuration ---------------------------------------------------
@@ -49,8 +49,8 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'glpi'
-html_theme_path = sphinx_glpi_theme.get_html_themes_path()
+html_theme = 'sphinx_rtd_theme'
+#html_theme_path = sphinx_rtd_theme.get_html_themes_path()
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".

diff --git a/docs/index.rst b/docs/index.rst
@@ -1,5 +1,5 @@
-The esgcet package for ESGF Publication - Version 5.2.0
-=========================================================
+The esgcet package for ESGF Publication - Version 5.2.1
+=======================================================
 
 Esgcet is a package of publisher commands for publishing to the `ESGF
 <https://esgf-node.llnl.gov/projects/esgf-llnl/>`_ search database.
@@ -8,15 +8,14 @@ Esgcet is a package of publisher commands for publishing to the `ESGF
 TL;DR
 -----
 
-if you have conda you can install the publisher wih the following into a fresh environment, and update to the latest version:
-::
-     conda create -n esgf-pub -c conda-forge -c esgf-forge esgcet
+If you have conda on a Linux system you can install the publisher wih the following into a fresh environment, and update to the latest version:::
+
+     conda create -n esgf-pub -c conda-forge pip cmor  # most commun
      conda activate esgf-pub
      pip install esgcet  
-     esgpublish --version #  Ensure you have upgraded to v5.2.0
+     esgpublish --version #  Ensure you have upgraded to v5.2.1
      esgpublish # will print the usage information.
 
-You may also look at the inital ``~/.esg/esg.yaml`` and update to fit your site configuration.
 
 .. toctree::
    :maxdepth: 2

diff --git a/docs/install.rst b/docs/install.rst
@@ -23,7 +23,7 @@ Use the following command to install ``esgcet`` into a previously created conda
 
     conda activate esgf-pub
     pip install esgcet 
-    esgpublish --version #  Ensure you have upgraded to v5.2.0
+    esgpublish --version #  Ensure you have upgraded to v5.2.1
 
 
 Installing esgcet via git
@@ -37,15 +37,26 @@ To install esgcet by cloning our github repository (useful if you want to modiy
     git checkout refactor-esgf # NOTE this is a temporary fix prior to a merge into the master branch
     cd src/python
     pip install -e .  # You can modify the source in place
-    esgpublish --version  # check v5.2.0 has been installed
+    esgpublish --version  # Confirm that v5.2.1 has been installed
+
+Now you will be able to call all commands in this package from any directory.  
+
 
-Now you will be able to call all commands in this package from any directory. A default config file, ``esg.yaml`` will populate in ``$HOME/.esg`` where ``$HOME`` is your home directory.
 
 NOTE: if you are intending to publish CMIP6 data, the publisher will run the PrePARE module to check all file metadata.  To enable this procedure, it is necessry to download CMOR tables before the publisher will successfully run. See those pages for more info.
 
 
 Config File (esg.yaml)
----------------------
+----------------------
+
+Starting with ``v5.2.0`` the ESGF Publisher uses a .yaml file for configuration.  Download a copy of the default config file ``esg.yaml`` to the default directory,
+ or see below regarding migrating a previous config  ::
+
+   wget https://raw.githubusercontent.com/ESGF/esg-publisher/refactor/src/python/esg.yaml
+   mkdir $HOME/.esg
+   cp esg.yaml $HOME/.esg
+
+
 
 The config file will contain the following settings:
 

diff --git a/docs/whatsnew.rst b/docs/whatsnew.rst
@@ -1,6 +1,10 @@
 Release Notes
 =============
 
+v5.2.1
+------
+* **BUGFIX**:  Missing `import` caused ``esgpublish`` calls to fail in most cases.
+
 v5.2.0
 ------
 

diff --git a/src/python/MANIFEST.in b/src/python/MANIFEST.in
@@ -0,0 +1 @@
+include esg.yaml
diff --git a/src/python/esgcet/__init__.py b/src/python/esgcet/__init__.py
@@ -1 +1 @@
-__version__ = "5.2.0"
+__version__ = "5.2.1"
diff --git a/src/python/esgcet/args.py b/src/python/esgcet/args.py
@@ -3,6 +3,7 @@
 import os
 import esgcet.esgmigrate as em
 import esgcet.logger as logger
+import esgcet
 import yaml
 
 log = logger.ESGPubLogger()

diff --git a/src/python/setup.py b/src/python/setup.py
@@ -16,13 +16,14 @@
 FULLPATH = HOME + '/.esg'
 DEFAULT_ESGINI = '/esg/config/esgcet'
 
-if not os.path.exists(FULLPATH):
-    os.makedirs(FULLPATH)
+# if not os.path.exists(FULLPATH):
+#     os.makedirs(FULLPATH)
 
-if os.path.exists(FULLPATH + "/esg.yaml"):
-    make_config = False
-else:
-    make_config = True
+# if os.path.exists(FULLPATH + "/esg.yaml"):
+#     make_config = False
+# else:
+
+make_config = True
 
 if make_config:
     setup(
@@ -53,9 +54,7 @@
                                           'esgupdate=esgcet.esgupdate:main',
                                           'esgmapconv=esgcet.esgmapconv:main',
                                           'esgmigrate=esgcet.migratecmd:main',
-                                          'esgunpublish=esgcet.esgunpublish:main']},
-        data_files=[(FULLPATH, ['esg.yaml'])]
-
+                                          'esgunpublish=esgcet.esgunpublish:main']}
     )
 else:
     setup(