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remove release procedure PR template, my username --> NOAA-GFDL everywhere i can find it
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.codecov.yml

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# Codecov configuration for ilaflott/fremorizer
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# Codecov configuration for NOAA-GFDL/fremorizer
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# Reference: https://docs.codecov.com/docs/codecovyml-reference
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coverage:

.github/PULL_REQUEST_TEMPLATE/release_procedure.md

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.github/workflows/publish_conda.yml

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activate-environment: base
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conda-remove-defaults: true
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miniforge-version: latest
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channels: conda-forge,noaa-gfdl,ilaflott
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channels: conda-forge,noaa-gfdl
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- name: Configure Conda
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run: |

CONTRIBUTING.md

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## **For Developers**
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* Developers are free to use this repository's `README.md` to familiarize with the CLI and save time from having to install any dependencies, but development within a Conda environment is heavily recommended regardless
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* Gain access to the repository with `git clone --recursive git@github.com:ilaflott/fremorizer.git` or your fork's link (recommended) and an SSH RSA key
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- Once inside the repository, developers can test local changes by running a `pip install .` inside of the root directory after activating a virtual environment, installing the fremorizer package locally with the newest local changes on top of the installed Conda fremorizer dependencies. the `-e` flag can be used for an editable installation
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* Gain access to the repository with `git clone --recursive git@github.com:NOAA-GFDL/fremor.git` or your fork's link (recommended) and an SSH RSA key
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- Once inside the repository, developers can test local changes by running a `pip install .` inside of the root directory after activating a virtual environment, installing the fremor package locally with the newest local changes on top of the installed Conda fremor dependencies. the `-e` flag can be used for an editable installation
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- Test as a normal user would use the CLI
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* Create a GitHub issue to reflect your contribution's background and reference it with Git commits
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### **Adding Tools From Other Repositories**
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* Currently, the solution to this task is to approach it using Conda packages. The tool that is being added must reside within a repository that contains a meta.yaml that includes Conda dependencies like the one in this repository and ideally a setup.py (may be subject to change due to deprecation) that may include any potentially needed pip dependencies
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- Once published as a Conda package, ideally on the [NOAA-GFDL channel](https://anaconda.org/NOAA-GFDL), an addition can be made to the "run" section under the "requirements" category in the meta.yaml of the fremorizer following the syntax `channel::package`
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- On pushes to the main branch, the [package](https://anaconda.org/ilaflott/fremorizer) will automatically be updated using the workflow file
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- Once published as a Conda package, ideally on the [NOAA-GFDL channel](https://anaconda.org/NOAA-GFDL), an addition can be made to the "run" section under the "requirements" category in the meta.yaml of the fremor following the syntax `channel::package`
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- On pushes to the main branch, the [package](https://anaconda.org/NOAA-GFDL/fremor) will automatically be updated using the workflow file
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### **MANIFEST.in**
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* In the case where non-python files like templates, examples, and outputs are to be included in the fremorizer package, MANIFEST.in can provide the solution. Ensure that the file exists within the correct folder, and add a line to the MANIFEST.in following [this syntax](https://setuptools.pypa.io/en/latest/userguide/miscellaneous.html)
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* In the case where non-python files like templates, examples, and outputs are to be included in the fremor package, MANIFEST.in can provide the solution. Ensure that the file exists within the correct folder, and add a line to the MANIFEST.in following [this syntax](https://setuptools.pypa.io/en/latest/userguide/miscellaneous.html)
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README.md

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# `fremorizer` / `fremor`
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`fremorizer` CMORizes FRE output with `CMOR`. It is a `conda` package and it's documentation can be found on
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[`readthedocs`](https://fremorizer.readthedocs.io/en/latest/).
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# `fremor`
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`fremor` CMORizes FRE output with `CMOR`. It is a `conda` package and it's documentation can be found on
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[`readthedocs`](https://fremor.readthedocs.io/en/latest/).
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[![Anaconda-Server Badge](https://anaconda.org/ilaflott/fremorizer/badges/version.svg)](https://anaconda.org/ilaflott/fremorizer)
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[![Anaconda-Server Badge](https://anaconda.org/ilaflott/fremorizer/badges/latest_release_date.svg)](https://anaconda.org/ilaflott/fremorizer)
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[![Anaconda-Server Badge](https://anaconda.org/ilaflott/fremorizer/badges/latest_release_relative_date.svg)](https://anaconda.org/ilaflott/fremorizer)
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[![Anaconda-Server Badge](https://anaconda.org/NOAA-GFDL/fremor/badges/version.svg)](https://anaconda.org/NOAA-GFDL/fremor)
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[![Anaconda-Server Badge](https://anaconda.org/NOAA-GFDL/fremor/badges/latest_release_date.svg)](https://anaconda.org/NOAA-GFDL/fremor)
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[![Anaconda-Server Badge](https://anaconda.org/NOAA-GFDL/fremor/badges/latest_release_relative_date.svg)](https://anaconda.org/NOAA-GFDL/fremor)
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[![pylint](https://img.shields.io/badge/pylint-%E2%89%A59.7-brightgreen)](https://github.com/ilaflott/fremorizer/actions/workflows/pylint.yml)
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[![codecov](https://codecov.io/gh/ilaflott/fremorizer/branch/main/graph/badge.svg)](https://codecov.io/gh/ilaflott/fremorizer)
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[![pylint](https://img.shields.io/badge/pylint-%E2%89%A59.7-brightgreen)](https://github.com/NOAA-GFDL/fremor/actions/workflows/pylint.yml)
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[![codecov](https://codecov.io/gh/NOAA-GFDL/fremor/branch/main/graph/badge.svg)](https://codecov.io/gh/NOAA-GFDL/fremor)
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[![publish_conda](https://github.com/ilaflott/fremorizer/actions/workflows/publish_conda.yml/badge.svg?branch=main)](https://github.com/ilaflott/fremorizer/actions/workflows/publish_conda.yml)
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[![readthedocs](https://app.readthedocs.org/projects/fremorizer/badge/?version=latest&style=flat)](https://fremorizer.readthedocs.io/en/latest/)
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[![pylint](https://github.com/ilaflott/fremorizer/actions/workflows/pylint.yml/badge.svg?branch=main)](https://github.com/ilaflott/fremorizer/actions/workflows/pylint.yml)
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[![publish_conda](https://github.com/NOAA-GFDL/fremor/actions/workflows/publish_conda.yml/badge.svg?branch=main)](https://github.com/NOAA-GFDL/fremor/actions/workflows/publish_conda.yml)
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[![readthedocs](https://app.readthedocs.org/projects/fremor/badge/?version=latest&style=flat)](https://fremor.readthedocs.io/en/latest/)
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[![pylint](https://github.com/NOAA-GFDL/fremor/actions/workflows/pylint.yml/badge.svg?branch=main)](https://github.com/NOAA-GFDL/fremor/actions/workflows/pylint.yml)
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`python3.11`:[![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)
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`python3.11`:[![3.11](https://github.com/NOAA-GFDL/fremor/actions/workflows/create_test_conda_env.yml/badge.svg)](https://github.com/NOAA-GFDL/fremor/actions/workflows/create_test_conda_env.yml?query=branch%3Amain+python-version%3A3.11)
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`python3.12`:[![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)
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`python3.12`:[![3.12](https://github.com/NOAA-GFDL/fremor/actions/workflows/create_test_conda_env.yml/badge.svg)](https://github.com/NOAA-GFDL/fremor/actions/workflows/create_test_conda_env.yml?query=branch%3Amain+python-version%3A3.12)
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`python3.13`:[![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)
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`python3.13`:[![3.13](https://github.com/NOAA-GFDL/fremor/actions/workflows/create_test_conda_env.yml/badge.svg)](https://github.com/NOAA-GFDL/fremor/actions/workflows/create_test_conda_env.yml?query=branch%3Amain+python-version%3A3.13)
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`python3.14`:[![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)
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`python3.14`:[![3.14](https://github.com/NOAA-GFDL/fremor/actions/workflows/create_test_conda_env.yml/badge.svg)](https://github.com/NOAA-GFDL/fremor/actions/workflows/create_test_conda_env.yml?query=branch%3Amain+python-version%3A3.14)
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## Background and Purpose
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`fremorizer` is a model output rewriter (CMORizer) for FRE/FMS based models and output. `fremorizer` (or `fremor` for short) is
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`fremor` is a model output rewriter (CMORizer) for FRE/FMS based models and output. `fremor` (or `fremor` for short) is
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geared for standardizing NOAA-GFDL datasets for further quality control checks, assessments and data publishing pipelines in the
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context of CMIP7 using the [`CMOR`](https://cmor.llnl.gov/) library.
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### Relationship to `fre-cli`
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`fremorizer` was originally the `fre.cmor` submodule of [`NOAA-GFDL/fre-cli`](https://github.com/NOAA-GFDL/fre-cli) and so stands
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`fremor` was originally the `fre.cmor` submodule of [`NOAA-GFDL/fre-cli`](https://github.com/NOAA-GFDL/fre-cli) and so stands
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on the shoulders of it's contributors, retaining it's general structure and lessons learned from it. Future re-integrations back
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into `fre-cli`, as a formal package dependency, are being assessed.
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### Contributors
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[![Contributors](https://contrib.rocks/image?repo=ilaflott/fremorizer)](https://github.com/ilaflott/fremorizer/graphs/contributors)
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[![Contributors](https://contrib.rocks/image?repo=NOAA-GFDL/fremor)](https://github.com/NOAA-GFDL/fremor/graphs/contributors)
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#### AI Disclaimer
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AI was heavily used in the creation of this repository, primarily `github`'s `copilot` with `Claude` (`opus4.6` `sonnet4.6`, and `haiku`), and `Gemini` and `Chat-GPT` models to a lesser extent, in agent mode. `Claude` and `Codex` agents have also contributed.
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If you're trying to gain access to `fremor` functionality as quickly as possible:
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```bash
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# the current post-release in main
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module load fremorizer/test
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module load fremor/test
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# a tagged version of fremorizer, post-releases will never be named modules
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module load fremorizer/X.Y.Z
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# a tagged version of fremor, post-releases will never be named modules
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module load fremor/X.Y.Z
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```
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### via `conda`
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If you have a path to a `fremorizer` environment you can activate it like so:
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If you have a path to a `fremor` environment you can activate it like so:
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```bash
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conda activate some/path/to/fremorizer_env
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conda activate some/path/to/fremor_env
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```
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If you want your own `fremorizer` environment:
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If you want your own `fremor` environment:
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```bash
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# the environment will be named fremorizer_en
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conda create -n fremorizer_env ilaflott::fremorizer
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# the environment will be named fremor_en
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conda create -n fremor_env NOAA-GFDL::fremor
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# see fremorizer_env in the list --> activate it by name
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# see fremor_env in the list --> activate it by name
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conda env list
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conda activate fremorizer_env
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conda activate fremor_env
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```bash
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conda install -c ilaflott fremorizer
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conda install -c NOAA-GFDL fremor
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conda install ilaflott::fremorizer
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conda install NOAA-GFDL::fremor
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### `pip` install source/checkout into a virtual environment (`conda`/`venv`)
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If you're trying to develop `fremorizer` capabilities, or edit the code to your liking in either a big or small way,
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If you're trying to develop `fremor` capabilities, or edit the code to your liking in either a big or small way,
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**this is for you**. This checks out the code, creates and activates an environment, installs into the environment,
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# omit --recursive if you don't want tables as submodules
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pytest fremor/tests/
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# fremorizer equivalent
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# fremor equivalent
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### WCRP Compliance Checking (under development)
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[![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)
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[![wcrp_compliance_check](https://github.com/NOAA-GFDL/fremor/actions/workflows/wcrp_compliance_check.yml/badge.svg?branch=main)](https://github.com/NOAA-GFDL/fremor/actions/workflows/wcrp_compliance_check.yml)
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The `wcrp_compliance_check` workflow validates CMORized NetCDF outputs against WCRP project
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specifications using [cc-plugin-wcrp](https://github.com/ESGF/cc-plugin-wcrp), a plugin for
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## Releases and Versioning
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`fremorizer` uses a post-release scheme to identify development beyond the latest tagged version and tie the current `main` branch to a
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`fremor` uses a post-release scheme to identify development beyond the latest tagged version and tie the current `main` branch to a
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`conda` package versioned as `develop`. To avoid confusion with `fre-workflows` and `fre-cli`, which often demand that the version tags
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match, `fremor`'s version format is `X.Y.Z[.post]`.
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### new published release procedure
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2. edit the version number in `fremor/_version.py` from the current one, to the desired version tag, remove `.post`, then open a PR. edit nothing else (usually).
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3. confirm the branch is functional by letting workflows finish, if you see green checks only, proceed. otherwise, stop and debug.
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4. draft a new release pointing to the PR branch, click release. the publishing workflow should trigger and finish, and you should see the `X.Y.Z` version in the conda channel.
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5. *releases in this repository are immutable*, **so even if the release workflow fails, breathe and move on to the next step.**
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6. edit the version number in `fremorizer/_version.py` to `X.Y.Z.post`, and merge the PR to main workflow steps passed. **`publish_conda`** will trigger again and upload what is in `main` under the `conda` version `develop` and `pip` version `X.Y.Z.post`
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6. edit the version number in `fremor/_version.py` to `X.Y.Z.post`, and merge the PR to main workflow steps passed. **`publish_conda`** will trigger again and upload what is in `main` under the `conda` version `develop` and `pip` version `X.Y.Z.post`

docs/contributing.rst

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.. code-block:: bash
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git clone --recursive git@github.com:NOAA-GFDL/fremor.git
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docs/contributing_to_docs.rst

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`at this gist <https://gist.github.com/SMotaal/24006b13b354e6edad0c486749171a70#sections>`__.
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With a PR to NOAA-GFDL/fremor (recommended)
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----------------------------------------------
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This approach is the easiest and most automated option for open-source contributors. It is completely
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* Make a branch, either with ``ilaflott/fremor`` as the remote, or your own fork.
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* Make a branch, either with ``NOAA-GFDL/fremor`` as the remote, or your own fork.
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* Edit a file any non-zero amount, commit that change to your branch, and push. If the branch is
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* Once the PR is opened, a ``readthedocs`` workflow will be run, even if that PR is in draft mode.

docs/usage.rst

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* `CMIP6 Tables <https://github.com/pcmdi/cmip6-cmor-tables>`_
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* `CMIP6 Controlled Vocabulary <https://github.com/WCRP-CMIP/CMIP6_CVs>`_
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* `PCMDI CMOR User Guide <http://cmor.llnl.gov/>`_
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* `fremor on GitHub <https://github.com/ilaflott/fremor>`_
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* `fremor on GitHub <https://github.com/NOAA-GFDL/fremor>`_
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* `fre-cli (upstream) <https://github.com/NOAA-GFDL/fre-cli>`_

fremor/_version.py

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"""
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import os
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version = os.getenv("GIT_DESCRIBE_TAG", "0.9.0.post")
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__version__ = version

meta.yaml

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about:
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home: https://github.com/ilaflott/fremorizer
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home: https://github.com/NOAA-GFDL/fremorizer
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license: Apache-2.0
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license_file: LICENSE.md
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summary: Model output rewriter (CMORizer) for FRE/FMS based models

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