more by-hand review, tweaks, version updates, submodule updates, etc.

.gitmodules

@@ -4,3 +4,4 @@
 [submodule "fremorizer/tests/test_files/cmip7-cmor-tables"]
 	path = fremorizer/tests/test_files/cmip7-cmor-tables
 	url = https://github.com/WCRP-CMIP/cmip7-cmor-tables.git
+	branch = DR-1.2.2.3-v1.0.5

README.md

@@ -1,4 +1,7 @@
 # `fremorizer`
+`fremorizer` CMORizes FRE output with `CMOR`. It is a `conda` package and it's documentation can be found on
+[`readthedocs`](https://fremorizer.readthedocs.io/en/latest/).
+
 [![Anaconda-Server Badge](https://anaconda.org/ilaflott/fremorizer/badges/version.svg)](https://anaconda.org/ilaflott/fremorizer)
 [![Anaconda-Server Badge](https://anaconda.org/ilaflott/fremorizer/badges/latest_release_date.svg)](https://anaconda.org/ilaflott/fremorizer)
 [![Anaconda-Server Badge](https://anaconda.org/ilaflott/fremorizer/badges/latest_release_relative_date.svg)](https://anaconda.org/ilaflott/fremorizer)
@@ -11,83 +14,98 @@
 [![codecov](https://codecov.io/gh/ilaflott/fremorizer/branch/main/graph/badge.svg)](https://codecov.io/gh/ilaflott/fremorizer)
 
 
-Simply put, `fremorizer` CMORizes FRE output with `CMOR`. 
+## Background and Purpose
+`fremorizer` is a model output rewriter (CMORizer) for FRE/FMS based models and output. It was originally the `fre.cmor`
+submodule of [`NOAA-GFDL/fre-cli`](https://github.com/NOAA-GFDL/fre-cli). `fremorizer` (or `fremor` for short) is geared
+for rewriting NOAA-GFDL datasets for further quality control checks, assessments and data publishing pipelines in the
+context of CMIP7 using the [`CMOR`](https://cmor.llnl.gov/) library.
 
-`fremorizer` is a `conda` package, it's documentation can be found on [`readthedocs`](https://fremorizer.readthedocs.io/en/latest/).
 
 
+## Installation / Access
 
-## Background and Purpose
-`fremorizer` is a model output rewriter (CMORizer) for FRE/FMS based models and output. It was originally the `fre.cmor` submodule of 
-[`NOAA-GFDL/fre-cli`](https://github.com/NOAA-GFDL/fre-cli). `fremorizer` (or `fremor` for short) is geared for rewriting NOAA-GFDL 
-datasets for further quality control checks, assessments and data publishing pipelines in the context of CMIP7 using the 
-[`CMOR`](https://cmor.llnl.gov/) library.
 
+### Requirements
 
+- `python>=3.11`
+- `click>=8.2`
+- `cmor>=3.14.2`
+- `netCDF4>=1.7`
+- `numpy>=2`
+- `pyyaml`
 
+For development and testing, `pylint`, `pytest`, and `pytest-cov` are all highly recommended as helpful additions.
 
-## Installation / Access
 
 ### via PPAN / modules (COMING SOON/TODO)
+If you're trying to gain access to `fremor` functionality as quickly as possible:
 ```bash
-# this will be whatever is in main of this repository (COMING SOON/TODO)
+# the current post-release in main
 module load fremorizer/test
 
-# this will be a tagged version of the package in this repository
-module load fremorizer/YYYY.XX.[ZZ]{-alpha,-beta}
+# a tagged version of fremorizer, post-releases will never be named modules
+module load fremorizer/X.Y.Z
 ```
 
-### From source/checkout into a virtual environment (`conda` or `venv`) with `pip`
-If you're trying to develop the package, or edit the code for contributing in either a big or small way, this is for you. If you're just
-trying to use `fremorizer` and you want to deal with as few technical details as possible, *this is not for you*. 
 
-Add `-e` to the `pip` step for an editable install. `--recursive` pulls in required configuration in the form of CMIP CMOR tables, and
-can be omitted if desired at the cost of local testing functionality out-of-box
+### via `conda`
+If you have a path to a `fremorizer` environment you can activate it like so:
 ```bash
-# this does work, right now
-git clone --recursive https://github.com/ilaflott/fremorizer.git
-cd fremorizer
-conda env create -f environment.yaml
-pip install . 
+conda activate some/path/to/fremorizer_env
 ```
 
-### Via `conda` (COMING SOON)
-If you just want an environment named `fremorizer` with the package:
+If you want your own `fremorizer` environment:
 ```bash
-# does not work yet, TODO
-conda create -n fremorizer noaa-gfdl::fremorizer
-conda activate fremorizer
+# the environment will be named fremorizer_en
+conda create -n fremorizer_env ilaflott::fremorizer
+
+# see fremorizer_env in the list --> activate it by name
+conda env list
+conda activate fremorizer_env
 ```
 
 or, if you've already activated a `conda` environment
 ```bash
-# does not work yet, TODO
-conda install -c noaa-gfdl fremorizer
+conda create -n empty_env
+conda activate empty_env
+conda install -c ilaflott fremorizer
 
-# does not work yet, TODO
 # equivalent syntax
-conda install noaa-gfdl::fremorizer
+conda install ilaflott::fremorizer
 ```
 
-## Usage
 
-### as a command line interface (CLI)
-The CLI entry point is `fremor`. It maps directly from the `fre cmor` subcommand:
+### `pip` install source/checkout into a virtual environment (`conda`/`venv`)
+If you're trying to develop `fremorizer` capabilities, or edit the code to your liking in either a big or small way,
+**this is for you**. This checks out the code, creates and activates an environment, installs into the environment,
+and runs all unit-tests and `pylint` checks:
 ```bash
-# past fre-cli command
-fre -vv -l logfile.txt cmor <COMMAND> [OPTIONS]
+# omit --recursive if you don't want tables as submodules
+git clone --recursive https://github.com/ilaflott/fremorizer.git
+cd fremorizer
 
-# fremorizer equivalent
-fremor -vv -l logfile.txt <COMMAND> [OPTIONS]
+# create an environment and install the local checkout
+conda env create -f environment.yaml
+conda actiavte fremorizer
+pip install -e . 
+
+# Run tests
+pytest fremorizer/tests/
+
+# Run linter
+pylint --rcfile pylintrc fremorizer/
 ```
 
-### as a `python` module
-Each CLI subcommand (`run`, `yaml`, etc.) maps to an API under under `fremor`, so the CLI functionality
-is equivalently available via `import` in scripts as a proper `python` module
 
-### Subcommands
 
+## Usage
+
+
+### as a command line interface (CLI)
+The CLI entry point is `fremor`, currently a suite of (currently) six routines for facillitating data preparation for
+CMIP7. 
 ```bash
+# The full list of subcommands
 fremor init      # Initialize CMOR configuration resources: generate template user config, fetch tables
 fremor find      # Find and print variables in MIP tables according to your variable lists or other input
 fremor varlist   # Create a simple variable list of netCDF files in a directory
@@ -96,85 +114,40 @@
 fremor run       # Lowest-level routine, no CMOR YAML needed, rewrites output files in a directory with CMOR
 ```
 
-For a concise overview of required inputs and sample commands, see the
-[CMOR Quickstart](docs/quickstart.rst).
-
-### Getting Started: Initialize CMOR Resources
-
-Before CMORizing data, you need an experiment configuration template and MIP tables.
-The `fremor init` command helps set up these resources:
-
+The CLI offers full logging and verbosity control independent of the command chosen:
 ```bash
-# Generate a CMIP6 experiment config template and fetch CMIP6 tables
-fremor init -m cmip6 -e exp_config.json -t cmip6-tables
-
-# Generate a CMIP7 experiment config template and fetch CMIP7 tables (fast mode)
-fremor init -m cmip7 -e exp_config.json -t cmip7-tables --fast
-
-# Fetch tables for a specific release tag
-fremor init -m cmip6 -t cmip6-tables --tag 6.9.33
+# verbosity and logging
+fremor -v  ...          # INFO level logging
+fremor -vv ...          # DEBUG level logging
+fremor -q  ...          # ERROR level only (quiet)
+fremor -l mylog.txt ... # Log to file (appends)
 ```
 
-This command:
-- Generates an experiment configuration JSON template with required CMIP metadata fields
-- Fetches official MIP tables from trusted GitHub repositories (CMIP6: `pcmdi/cmip6-cmor-tables`, CMIP7: `WCRP-CMIP/cmip7-cmor-tables`)
-- Supports both `git clone` (default) and `curl` (`--fast`) methods for downloading official configurations
-
-### Verbosity and Logging
-
+If you've used the previous `fre cmor` command, there is a direct mapping of syntax:
 ```bash
-fremor -v run ...        # INFO level logging
-fremor -vv run ...       # DEBUG level logging
-fremor -q run ...        # ERROR level only (quiet)
-fremor -l log.txt run ...  # Log to file (appends)
-```
-
-### Example: CMORize ocean data
+# past fre-cli command
+fre -vv -l logfile.txt cmor <COMMAND> [OPTIONS]
 
-```bash
-fremor run \
-    -d /path/to/input/netcdf/dir \
-    -l /path/to/varlist.json \
-    -r /path/to/CMIP6_Omon.json \
-    -p /path/to/exp_config.json \
-    -o /path/to/output/dir
+# fremorizer equivalent
+fremor -vv -l logfile.txt <COMMAND> [OPTIONS]
 ```
 
-## Requirements
-
-- `python>=3.11`
-- `click>=8.2`
-- `cmor>=3.14.2`
-- `netCDF4>=1.7`
-- `numpy>=2`
-- `pyyaml`
 
-For development and testing, `pylint`, `pytest`, and `pytest-cov` are all highly recommended as helpful additions.
+### as a `python` module
+Each CLI subcommand (`run`, `yaml`, etc.) maps to an API under under `fremor`, so the CLI functionality
+is equivalently available via `import` in scripts as a proper `python` module
 
-## Development
 
-```bash
-# Checkout code
-git clone --recursive https://github.com/ilaflott/fremorizer.git
-cd fremorizer
 
-# Create a conda environment
-conda env create -f environment.yaml
-conda activate fremorizer
+## Getting started
+For an overview of required inputs and sample commands, see the [CMOR Quickstart](docs/quickstart.rst).
 
-# Install in editable mode
-pip install -e .
 
-# Run tests
-pytest fremorizer/tests/
 
-# Run linter
-pylint --rcfile pylintrc fremorizer/
-```
+## CI/CD Workflows and QA
 
-## Quality Assurance
 
-### WCRP Compliance Checking
+### WCRP Compliance Checking (under development)
 
 [![wcrp_compliance_check](https://github.com/ilaflott/fremorizer/actions/workflows/wcrp_compliance_check.yml/badge.svg?branch=main)](https://github.com/ilaflott/fremorizer/actions/workflows/wcrp_compliance_check.yml)
 
@@ -193,28 +166,27 @@
 2. Select the `wcrp_compliance_check` workflow run
 3. Download the `wcrp-compliance-reports` artifact
 
-### pipeline badges
+
+### `conda` environment tests
 
 | Python 3.11 | Python 3.12 | Python 3.13 | Python 3.14 |
 |-------------|-------------|-------------|-------------|
 | [![3.11](https://github.com/ilaflott/fremorizer/actions/workflows/create_test_conda_env.yml/badge.svg)](https://github.com/ilaflott/fremorizer/actions/workflows/create_test_conda_env.yml?query=branch%3Amain+python-version%3A3.11) | [![3.12](https://github.com/ilaflott/fremorizer/actions/workflows/create_test_conda_env.yml/badge.svg)](https://github.com/ilaflott/fremorizer/actions/workflows/create_test_conda_env.yml?query=branch%3Amain+python-version%3A3.12) | [![3.13](https://github.com/ilaflott/fremorizer/actions/workflows/create_test_conda_env.yml/badge.svg)](https://github.com/ilaflott/fremorizer/actions/workflows/create_test_conda_env.yml?query=branch%3Amain+python-version%3A3.13) | [![3.14](https://github.com/ilaflott/fremorizer/actions/workflows/create_test_conda_env.yml/badge.svg)](https://github.com/ilaflott/fremorizer/actions/workflows/create_test_conda_env.yml?query=branch%3Amain+python-version%3A3.14) |
 
-## License
 
+
+## License
 Apache License 2.0 — see [LICENSE.md](LICENSE.md)
 
-## Conda-forge feedstock
 
-See `CONDA_FORGE_FEEDSTOCK_PLAN.md` for the steps and follow-up tasks to submit and maintain the conda-forge feedstock for `fremorizer`.
 
 ## Releases and Versioning
-
 `fremorizer` uses a post-release scheme to identify development beyond the latest tagged version and tie the current `main` branch to a
 `conda` package versioned as `develop`. To avoid confusion with `fre-workflows` and `fre-cli`, which often demand that the version tags 
 match, `fremorizer`'s version format is `X.Y.Z[.post]`. 
 
-### new published release procedure 
 
+### new published release procedure 
 To publish new release carefully follow the below procedure:
 1. create a new branch off of `main`, which is already published to `conda` under `develop`/the previous tagged version + `.post`
 2. edit the version number in `fremorizer/_version.py` from the current one, to the desired version tag, remove `.post`, then open a PR. edit nothing else (usually).

environment.yaml

@@ -5,7 +5,7 @@ channels:
 dependencies:
   - python>=3.11
   - conda-forge::click>=8.2
-  - conda-forge::cmor>=3.14
+  - conda-forge::cmor>=3.14.2
   - conda-forge::netcdf4>=1.7
   - conda-forge::numpy>=2
   - conda-forge::pyyaml

fremorizer/cli.py

@@ -271,8 +271,8 @@ def varlist(dir_targ, output_variable_list, mip_table):
               help="Temporal frequency string, e.g. 'monthly', 'daily'. Default 'monthly'.")
 @click.option("--chunk", type=str, default="5yr",
               help="Time chunk string, e.g. '5yr', '10yr'. Default '5yr'.")
-@click.option("--grid", type=str, default="g99",
-              help="Grid label anchor name, e.g. 'g99', 'gn'. Default 'g99'.")
+@click.option("--grid", type=str, default="g999",
+              help="Grid label anchor name, e.g. 'g999', 'gn'. Default 'g999'.")
 @click.option("--overwrite", is_flag=True, default=False,
               help="Overwrite existing variable list files.")
 @click.option("--calendar", type=str, default="noleap",

fremorizer/cmor_config.py

@@ -61,7 +61,7 @@ def cmor_config_subtool(
         varlist_dir: str,
         freq: str = 'monthly',
         chunk: str = '5yr',
-        grid: str = 'g99',
+        grid: str = 'g999',
         overwrite: bool = False,
         calendar_type: str = 'noleap'
 ):
@@ -90,7 +90,7 @@ def cmor_config_subtool(
     :type freq: str
     :param chunk: Time chunk string, e.g. '5yr', '10yr'. Default '5yr'.
     :type chunk: str
-    :param grid: Grid label anchor name, e.g. 'g99', 'gn'. Default 'g99'.
+    :param grid: Grid label anchor name, e.g. 'g999', 'gn'. Default 'g999'.
     :type grid: str
     :param overwrite: If True, overwrite existing variable list files. Default False.
     :type overwrite: bool

fremorizer/cmor_init.py

@@ -118,9 +118,7 @@ def _cmip7_exp_config_template():
         "tracking_prefix": "hdl:21.14107",
         "_cmip7_option": 1,
         "mip_era": "CMIP7",
-        "parent_mip_era": "CMIP7",
         "activity_id": "CMIP",
-        "parent_activity_id": "CMIP",
         "institution": "",
         "institution_id": "",
         "source": "",
@@ -129,21 +127,17 @@ def _cmip7_exp_config_template():
         "experiment_id": "",
         "sub_experiment": "none",
         "sub_experiment_id": "none",
-        "parent_source_id": "",
-        "parent_experiment_id": "",
         "realization_index": "r1",
         "initialization_index": "i1",
         "physics_index": "p1",
         "forcing_index": "f1",
         "run_variant": "",
-        "parent_variant_label": "",
-        "parent_time_units": "",
         "branch_method": "no parent",
         "branch_time_in_child": 0.0,
         "branch_time_in_parent": 0.0,
         "calendar": "",
         "grid": "PLACEHOLD",
-        "grid_label": "g99",
+        "grid_label": "g999",
         "frequency": "",
         "region": "",
         "nominal_resolution": "",

fremorizer/tests/test_cli.py

@@ -223,7 +223,7 @@ def test_cli_fremor_run_cmip7_case1(cli_sos_nc_file, tmp_path): # pylint: disabl
                                             "--exp_config", str(EXP_CONFIG_CMIP7),
                                             "--outdir", outdir,
                                             "--calendar", "julian",
-                                            "--grid_label", "g99",
+                                            "--grid_label", "g999",
                                             "--grid_desc", "FOO_BAR_PLACEHOLD",
                                             "--nom_res", "10000 km" ] )
     assert result.exit_code == 0, f'cmip7 case1 failed: {result.output}'
@@ -245,7 +245,7 @@ def test_cli_fremor_run_cmip7_case2(cli_sosv2_nc_file, tmp_path): # pylint: disa
                                             "--exp_config", str(EXP_CONFIG_CMIP7),
                                             "--outdir", outdir,
                                             "--calendar", "julian",
-                                            "--grid_label", "g99",
+                                            "--grid_label", "g999",
                                             "--grid_desc", "FOO_BAR_PLACEHOLD",
                                             "--nom_res", "10000 km" ] )
     assert result.exit_code == 0, f'cmip7 case2 failed: {result.output}'