diff --git a/.github/workflows/check-valid-env-dev.yml b/.github/workflows/check-valid-env-dev.yml new file mode 100644 index 0000000..1bfd58e --- /dev/null +++ b/.github/workflows/check-valid-env-dev.yml @@ -0,0 +1,19 @@ +name: env-dev.yml +on: + pull_request: + paths: + - 'env-dev.yml' +jobs: + check: + name: Check + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + + - name: Env Valid + uses: mamba-org/setup-micromamba@f8b8a1e23a26f60a44c853292711bacfd3eac822 #v1.9.0 + with: + micromamba-version: '1.5.8-0' + environment-file: env-dev.yml + environment-name: test-access-ram-environment-dev + generate-run-shell: false \ No newline at end of file diff --git a/.github/workflows/check-valid-env.yml b/.github/workflows/check-valid-env.yml new file mode 100644 index 0000000..b617bee --- /dev/null +++ b/.github/workflows/check-valid-env.yml @@ -0,0 +1,19 @@ +name: env.yml +on: + pull_request: + paths: + - 'env.yml' +jobs: + check: + name: Check + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + + - name: Env Valid + uses: mamba-org/setup-micromamba@f8b8a1e23a26f60a44c853292711bacfd3eac822 #v1.9.0 + with: + micromamba-version: '1.5.8-0' + environment-file: env.yml + environment-name: test-access-ram-environment + generate-run-shell: false \ No newline at end of file diff --git a/.github/workflows/validate-json.yml b/.github/workflows/validate-json.yml new file mode 100644 index 0000000..9ffcec6 --- /dev/null +++ b/.github/workflows/validate-json.yml @@ -0,0 +1,11 @@ +name: Validate JSON files +on: + pull_request: + paths: + - '**.json' +jobs: + validate: + name: Validate + uses: access-nri/actions/.github/workflows/validate-json.yml@main + with: + src: "config" \ No newline at end of file diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 0000000..12739d5 --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,22 @@ +{ + "workbench.colorCustomizations": { + "activityBar.activeBackground": "#5820ae", + "activityBar.background": "#5820ae", + "activityBar.foreground": "#e7e7e7", + "activityBar.inactiveForeground": "#e7e7e799", + "activityBarBadge.background": "#1b0e05", + "activityBarBadge.foreground": "#e7e7e7", + "commandCenter.border": "#e7e7e799", + "sash.hoverBorder": "#5820ae", + "statusBar.background": "#421883", + "statusBar.foreground": "#e7e7e7", + "statusBarItem.hoverBackground": "#5820ae", + "statusBarItem.remoteBackground": "#421883", + "statusBarItem.remoteForeground": "#e7e7e7", + "titleBar.activeBackground": "#421883", + "titleBar.activeForeground": "#e7e7e7", + "titleBar.inactiveBackground": "#42188399", + "titleBar.inactiveForeground": "#e7e7e799" + }, + "peacock.remoteColor": "#421883" +} \ No newline at end of file diff --git a/COPYRIGHT.txt b/COPYRIGHT.txt new file mode 100644 index 0000000..c487d89 --- /dev/null +++ b/COPYRIGHT.txt @@ -0,0 +1,13 @@ + Copyright 2022 ACCESS-NRI + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. \ No newline at end of file diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..261eeb9 --- /dev/null +++ b/LICENSE @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/README.md b/README.md new file mode 100644 index 0000000..9522c6f --- /dev/null +++ b/README.md @@ -0,0 +1,50 @@ +# access-ram-condaenv + +This repository is created taking [payu-condaenv](https://github.com/ACCESS-NRI/payu-condaenv) as a reference. + +## Overview + +This repository is responsible for building, packaging and deploying the environment needed to run the [replace_landsurface](https://github.com/ACCESS-NRI/replace_landsurface) python scripts, as part of [ACCESS-RAM3](https://github.com/ACCESS-NRI/ACCESS-RAM3). +This environment is created as a [`micromamba` environment](https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html). + +## Usage + +### Triggering a Deployment + +In order to trigger a deployment, the following steps must be followed: + +- Open a PR modifying the `env.yml` file. +- The `env.yml` will be checked for validity. +- When the PR is merged, the `env.yml` will be used to create a `micromamba` environment. This is then packaged using `conda-pack`, and deployed to the appropriate targets (eg. Gadi). + +### Using the Deployed Environment + +On all of the deployment targets, the deployed environment can be activated using Environment Modules. + +#### Gadi + +1. Make sure you're a member of the `` project! If not, see [how to join an NCI project](https://access-hive.org.au/getting_started/first_steps/#join-relevant-nci-projects). + > [!IMPORTANT] + > Make sure you do not have another conda environment active: either run `conda deactivate` or `module unload` any modules that are using conda. + +2. Once you are a member, run the following: + + ```bash + module use /g/data//modules + module load access-ram3 + ``` + +You are set to run ACCESS-RAM3. + +## Notes + +### On Future Deployment Environments + +New deployment environments must be created as a GitHub Environment and also have an entry in the [`config/deployment-environment.json`](https://github.com/ACCESS-NRI/access-ram-condaenv/blob/main/config/deployment-environment.json) file. + +### Deploying locally + +To deploy locally, you can use the assets created during the release. [Releases are found here](https://github.com/ACCESS-NRI/access-ram-condaenv/releases). Specifically: + +- To use the compressed environment (which doesn't require conda or python) you can run `tar -xzf access-ram.tar.gz access-ram` and then `./access-ram/bin/activate` to activate the environment. +- To use the lockfile, you can run `micromamba create -n environment-name -f access-ram.conda-lock.yml` with an appropriate install of `micromamba`. diff --git a/config/deployment-environment.json b/config/deployment-environment.json new file mode 100644 index 0000000..5e57e95 --- /dev/null +++ b/config/deployment-environment.json @@ -0,0 +1,6 @@ +{ + "$schema": "./deployment-environment.schema.json", + "environments": [ + "Gadi" + ] +} \ No newline at end of file diff --git a/config/deployment-environment.schema.json b/config/deployment-environment.schema.json new file mode 100644 index 0000000..0519787 --- /dev/null +++ b/config/deployment-environment.schema.json @@ -0,0 +1,19 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "Deployment Environments", + "description": "A list of deployment targets that are supported", + "type": "object", + "properties": { + "$schema": { + "type": "string" + }, + "environments": { + "type": "array", + "items": { + "type": "string" + } + } + }, + "required": ["environments"], + "additionalProperties": false +} \ No newline at end of file diff --git a/env-dev.yml b/env-dev.yml new file mode 100644 index 0000000..76fe706 --- /dev/null +++ b/env-dev.yml @@ -0,0 +1,17 @@ +name: access-ram-dev +channels: + - accessnri + - coecms + - conda-forge +dependencies: + - hypothesis + - ipykernel + - numpy=1.23.4 # https://stackoverflow.com/a/75148219/21024780 + - pip + - python=3.10 + - pytest + - pytest-cov + - scitools-iris + - xarray + - pip: + - mule @ git+https://github.com/metomi/mule@cce4b99c7046217b1ec1192118a786636e0d8e54#subdirectory=mule diff --git a/env.yml b/env.yml new file mode 100644 index 0000000..438476d --- /dev/null +++ b/env.yml @@ -0,0 +1,13 @@ +name: access-ram +channels: + - accessnri + - coecms + - conda-forge +dependencies: + - numpy=1.23.4 # https://stackoverflow.com/a/75148219/21024780 + - pip + - python=3.10 + - scitools-iris + - xarray + - pip: + - mule @ git+https://github.com/metomi/mule@cce4b99c7046217b1ec1192118a786636e0d8e54#subdirectory=mule diff --git a/modules/.common b/modules/.common new file mode 100644 index 0000000..eef2c7f --- /dev/null +++ b/modules/.common @@ -0,0 +1,51 @@ +#%Module1.0 + +# This is adapted from hh5's modulefiles for activating conda environments +# using modules (see /g/data/hh5/public/modules/conda/.common.v2) + +module-whatis {Activate access-ram micromamba environment (https://github.com/ACCESS-NRI/access-ram-condaenv)} +conflict access-ram + +# Name of this module's environment +set envname [module-info name] + +# Get the environment variables from activate script +set payuenv [exec /bin/env -i {{MODULE_LOCATION}}/env.sh $envname] + +# Convert the environment into module commands +set lines [split $payuenv '\n'] +foreach line $lines { + regexp {^([^=]*)=(.*)} $line -> key value + + # Exclude $PWD and $_ + if {[lsearch -exact {MODULEPATH PWD _} $key] >= 0} { + continue + } + + # Is this some sort of path? + if {[string match UDUNITS2_XML_PATH $key]} { + # This is actually a single path + setenv $key $value + continue + } elseif {[string match *?PATH $key]} { + # A *PATH variable to be prepended with a ':' + prepend-path $key $value + continue + } elseif {[lsearch {_LMFILES_ LOADEDMODULES} $key] >= 0} { + # Modulefile stuff that works like a path + prepend-path $key $value + continue + } elseif {[string match PATH $key]} { + # PATH itself (strip out the system paths to keep ordering correct) + prepend-path $key [regsub {:/usr/bin:/bin} $value {}] + continue + } + + # Otherwise set an environment var + setenv $key $value +} + +setenv LC_ALL en_AU.utf8 + +# Disable including libraries from ~/.local +setenv PYTHONNOUSERSITE x \ No newline at end of file diff --git a/modules/env.sh b/modules/env.sh new file mode 100755 index 0000000..0045d4a --- /dev/null +++ b/modules/env.sh @@ -0,0 +1,6 @@ +#!/bin/bash +# Prints the environment variables when activating un-packed environment +export PATH=/usr/bin:/bin + +source {{APPS_LOCATION}}/$1/bin/activate +/bin/env \ No newline at end of file