From c6ac4478c4deaacce465c285242de534514dc5dd Mon Sep 17 00:00:00 2001 From: Ahmed Ilyas Date: Mon, 23 Sep 2024 16:05:35 +0200 Subject: [PATCH] Update to the new distro mechanism (#23) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update to the new distro mechanism * Revert tip * Update configs/nomad.yaml Co-authored-by: Hampus Näsström * Add generate dep script * Add volume and git instruction * Delete nomad.yaml * Add nomad.yaml to Dockerfile * Update docker image * Add run scripts * Add all examples * Update lockfile * Example upload scripts * Improve docker build step * Delete version number * Update readme * Copy jupyterhub config * Separate build step and lock step * Use python3.12 * Constraint hyperspy * Avoid fail fast * Change image url * Update permissions * Remove example uploads * Use uv project interface * Move permissions in GA * Use static versioning * Include plugins extra * Delete extra scripts * Install plugins in jupyterhub * Use repo name * Optimize dockerfile * Fix warning --------- Co-authored-by: Hampus Näsström Co-authored-by: github-actions --- .github/workflows/build-app.yml | 94 + .github/workflows/docker-publish.yml | 62 - .github/workflows/initialize.yml | 15 +- .volumes/fs/north/users/.gitignore | 2 + .volumes/fs/public/.gitignore | 2 + .volumes/fs/staging/.gitignore | 2 + .volumes/fs/tmp/.gitignore | 2 + .volumes/mongo/.gitignore | 2 + Dockerfile | 156 +- configs/nginx.conf | 82 + configs/nomad.yaml | 29 + docker-compose.yaml | 12 +- nomad-oasis.zip | Bin 4916 -> 0 bytes nomad.yaml | 34 - plugins.txt | 2 - pyproject.toml | 52 + scripts/run-worker.sh | 3 + scripts/run.sh | 3 + template_README.md | 92 +- uv.lock | 7498 ++++++++++++++++++++++++++ 20 files changed, 7993 insertions(+), 151 deletions(-) create mode 100644 .github/workflows/build-app.yml delete mode 100644 .github/workflows/docker-publish.yml create mode 100644 .volumes/fs/north/users/.gitignore create mode 100644 .volumes/fs/public/.gitignore create mode 100644 .volumes/fs/staging/.gitignore create mode 100644 .volumes/fs/tmp/.gitignore create mode 100644 .volumes/mongo/.gitignore create mode 100644 configs/nginx.conf create mode 100644 configs/nomad.yaml delete mode 100644 nomad-oasis.zip delete mode 100644 nomad.yaml delete mode 100644 plugins.txt create mode 100644 pyproject.toml create mode 100755 scripts/run-worker.sh create mode 100755 scripts/run.sh create mode 100644 uv.lock diff --git a/.github/workflows/build-app.yml b/.github/workflows/build-app.yml new file mode 100644 index 0000000..ee990ed --- /dev/null +++ b/.github/workflows/build-app.yml @@ -0,0 +1,94 @@ +# Build and publish a Docker image. +name: Build and publish docker images + +on: + push: + branches: ["main"] + # Publish semver tags as releases. + tags: ["v*.*.*"] + pull_request: + branches: ["main"] + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +env: + REGISTRY: ghcr.io + +permissions: + contents: write + packages: write + attestations: write + id-token: write + +jobs: + # Job 1: Update Lock File + update-lockfile: + name: Update Python Lock File + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + with: + ref: ${{ github.head_ref || github.ref_name }} + submodules: true + + - name: Install uv + uses: astral-sh/setup-uv@v2 + + - uses: actions/setup-python@v5 + with: + python-version: "3.11" + + - name: Update lock file + run: uv lock --upgrade-package nomad-lab + + # Commits any changes made to the lockfile + - name: Commit lock file changes + run: | + git config --global user.name github-actions + git config --global user.email github-actions@github.com + git add uv.lock + if [[ `git status --porcelain` ]]; then + git commit -m "Update lockfile" + git push origin -o ci.skip # prevent triggering the pipeline again + fi + + # Job 2: Build and Push Docker Image + docker-publish: + name: Build Docker Image + runs-on: ubuntu-latest + needs: update-lockfile + + strategy: + fail-fast: false + matrix: + service: [app, jupyter] + steps: + - uses: actions/checkout@v4 + with: + ref: ${{ github.head_ref || github.ref_name }} + submodules: true + + - uses: docker/setup-buildx-action@v3 + + - uses: docker/login-action@v3 + with: + registry: ${{ env.REGISTRY }} + username: ${{ github.actor }} + password: ${{ secrets.GITHUB_TOKEN }} + + - name: Extract Docker metadata + id: meta + uses: docker/metadata-action@v5 + with: + images: ${{ env.REGISTRY }}/${{ github.repository }}/${{ matrix.service }} + + - name: Build and push Docker image + uses: docker/build-push-action@v5 + with: + context: . + cache-from: type=gha + cache-to: type=gha,mode=max + target: ${{ matrix.service == 'jupyter' && 'jupyter' || 'final' }} + push: ${{ github.event_name != 'pull_request' }} + tags: ${{ steps.meta.outputs.tags }} + labels: ${{ steps.meta.outputs.labels }} diff --git a/.github/workflows/docker-publish.yml b/.github/workflows/docker-publish.yml deleted file mode 100644 index ac014b8..0000000 --- a/.github/workflows/docker-publish.yml +++ /dev/null @@ -1,62 +0,0 @@ -name: Docker - -# This workflow uses actions that are not certified by GitHub. -# They are provided by a third-party and are governed by -# separate terms of service, privacy policy, and support -# documentation. - -on: - schedule: - - cron: '00 03 * * 0' - push: - branches: [ "main" ] - # Publish semver tags as releases. - tags: [ 'v*.*.*' ] - pull_request: - branches: [ "main" ] - # Allows you to run this workflow manually from the Actions tab - workflow_dispatch: - -env: - REGISTRY: ghcr.io - IMAGE_NAME: ${{ github.repository }} - - -jobs: - build: - runs-on: ubuntu-latest - permissions: - contents: read - packages: write - steps: - - name: Checkout repository - uses: actions/checkout@v3 - with: - submodules: True - - - name: Set up Docker Buildx - uses: docker/setup-buildx-action@v3 - - - name: Login - uses: docker/login-action@v3 - with: - registry: ${{ env.REGISTRY }} - username: ${{ github.actor }} - password: ${{ secrets.GITHUB_TOKEN }} - - - name: Extract Docker metadata - id: meta - uses: docker/metadata-action@v5 - with: - images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }} - - - name: Build and push - id: build-and-push - uses: docker/build-push-action@v5 - with: - context: . - push: ${{ github.event_name != 'pull_request' }} - tags: ${{ steps.meta.outputs.tags }} - labels: ${{ steps.meta.outputs.labels }} - cache-from: type=gha - cache-to: type=gha,mode=max \ No newline at end of file diff --git a/.github/workflows/initialize.yml b/.github/workflows/initialize.yml index f39b0f1..38b6695 100644 --- a/.github/workflows/initialize.yml +++ b/.github/workflows/initialize.yml @@ -1,4 +1,3 @@ - name: Template Repository Initialization on: @@ -27,18 +26,22 @@ jobs: - name: Update README run: | sed -i "s|GITHUB_REPOSITORY_OWNER|${{ github.repository_owner }}|g" template_README.md + sed -i "s|GITHUB_REPOSITORY_NAME|${{ github.event.repository.name }}|g" template_README.md sed -i "s|GITHUB_REPOSITORY|${{ github.repository }}|g" template_README.md + sed -i "s|GITHUB_REPOSITORY_NAME|${{ github.event.repository.name }}|g" template_README.md mv template_README.md README.md - + # Replaces the template repository name in the docker config file with the new one - name: Update docker-compose.yaml run: | export image_name="${{ github.repository }}" sed -i "s|fairmat-nfdi/nomad-distribution-template|${image_name,,}|g" docker-compose.yaml - mkdir nomad-oasis - cp docker-compose.yaml nomad-oasis - zip -ur nomad-oasis.zip nomad-oasis - rm -r nomad-oasis + + # Replaces the template repository name in the nomad config with the new one + - name: Update nomad.yaml + run: | + export image_name="${{ github.repository }}" + sed -i "s|fairmat-nfdi/nomad-distribution-template|${image_name,,}|g" configs/nomad.yaml # Deletes this workflow file to prevent it from running on branch creation - name: Delete initialization workflow diff --git a/.volumes/fs/north/users/.gitignore b/.volumes/fs/north/users/.gitignore new file mode 100644 index 0000000..d6b7ef3 --- /dev/null +++ b/.volumes/fs/north/users/.gitignore @@ -0,0 +1,2 @@ +* +!.gitignore diff --git a/.volumes/fs/public/.gitignore b/.volumes/fs/public/.gitignore new file mode 100644 index 0000000..d6b7ef3 --- /dev/null +++ b/.volumes/fs/public/.gitignore @@ -0,0 +1,2 @@ +* +!.gitignore diff --git a/.volumes/fs/staging/.gitignore b/.volumes/fs/staging/.gitignore new file mode 100644 index 0000000..d6b7ef3 --- /dev/null +++ b/.volumes/fs/staging/.gitignore @@ -0,0 +1,2 @@ +* +!.gitignore diff --git a/.volumes/fs/tmp/.gitignore b/.volumes/fs/tmp/.gitignore new file mode 100644 index 0000000..d6b7ef3 --- /dev/null +++ b/.volumes/fs/tmp/.gitignore @@ -0,0 +1,2 @@ +* +!.gitignore diff --git a/.volumes/mongo/.gitignore b/.volumes/mongo/.gitignore new file mode 100644 index 0000000..d6b7ef3 --- /dev/null +++ b/.volumes/mongo/.gitignore @@ -0,0 +1,2 @@ +* +!.gitignore diff --git a/Dockerfile b/Dockerfile index 2ece209..1335771 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,8 +1,150 @@ -FROM gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-fair:develop -USER root -RUN apt-get update -RUN apt-get -y install git +# syntax=docker/dockerfile:1 + +# Comments are provided throughout this file to help you get started. +# If you need more help, visit the Dockerfile reference guide at +# https://docs.docker.com/engine/reference/builder/ + +ARG PYTHON_VERSION=3.12 + +FROM python:${PYTHON_VERSION}-slim AS base + +# Keeps Python from buffering stdout and stderr to avoid situations where +# the application crashes without emitting any logs due to buffering. +ENV PYTHONUNBUFFERED=1 +ENV VIRTUAL_ENV=/opt/venv \ + PATH="/opt/venv/bin:$PATH" \ + UV_LINK_MODE=copy \ + UV_PROJECT_ENVIRONMENT=/opt/venv + +# Final stage to create the runnable image with minimal size +FROM base AS base_final + +WORKDIR /app + +RUN apt-get update \ + && apt-get install --yes --quiet --no-install-recommends \ + libgomp1 \ + libmagic1 \ + curl \ + zip \ + unzip \ + nodejs \ + npm \ + && npm install -g configurable-http-proxy@^4.2.0 \ + # clean cache and logs + && rm -rf /var/lib/apt/lists/* /var/log/* /var/tmp/* ~/.npm + +# Activate the virtualenv in the container +# See here for more information: +# https://pythonspeed.com/articles/multi-stage-docker-python/ +ENV PATH="/opt/venv/bin:$PATH" + +# Create a non-privileged user that the frenrug will run under. +# See https://docs.docker.com/develop/develop-images/dockerfile_best-practices/#user +ARG UID=1000 +RUN adduser \ + --disabled-password \ + --gecos "" \ + --home "/nonexistent" \ + --shell "/sbin/nologin" \ + --no-create-home \ + --uid "${UID}" \ + nomad + +FROM base AS builder + +# Prevents Python from writing pyc files. +ENV PYTHONDONTWRITEBYTECODE=1 + +ENV RUNTIME=docker + +WORKDIR /app + +RUN apt-get update \ + && apt-get install --yes --quiet --no-install-recommends \ + libgomp1 \ + libmagic1 \ + file \ + gcc \ + build-essential \ + curl \ + zip \ + unzip \ + git \ + && rm -rf /var/lib/apt/lists/* + +# Create a non-privileged user that the frenrug will run under. +# See https://docs.docker.com/develop/develop-images/dockerfile_best-practices/#user +ARG UID=1000 +RUN adduser \ + --disabled-password \ + --gecos "" \ + --home "/nonexistent" \ + --shell "/sbin/nologin" \ + --no-create-home \ + --uid "${UID}" \ + nomad + + +# Install UV +COPY --from=ghcr.io/astral-sh/uv:0.4 /uv /bin/uv + +RUN --mount=type=cache,target=/root/.cache/uv \ + --mount=type=bind,source=uv.lock,target=uv.lock \ + --mount=type=bind,source=pyproject.toml,target=pyproject.toml \ + uv sync --extra plugins --frozen --no-install-project + + +COPY scripts ./scripts + +FROM base_final AS final + +COPY --chown=nomad:1000 --from=builder /opt/venv /opt/venv +COPY --chown=nomad:1000 scripts/run.sh . +COPY --chown=nomad:1000 scripts/run-worker.sh . +COPY configs/nomad.yaml nomad.yaml + +RUN mkdir -p /app/.volumes/fs \ + && chown -R nomad:1000 /app \ + && chown -R nomad:1000 /opt/venv \ + && mkdir nomad \ + && cp /opt/venv/lib/python3.12/site-packages/nomad/jupyterhub_config.py nomad/ + USER nomad -COPY plugins.txt plugins.txt -RUN pip install -r plugins.txt -COPY nomad.yaml nomad.yaml \ No newline at end of file + +# The application ports +EXPOSE 8000 +EXPOSE 9000 + +VOLUME /app/.volumes/fs + + +FROM jupyter/datascience-notebook:lab-3.6.2 AS jupyter + +# Fix: https://github.com/hadolint/hadolint/wiki/DL4006 +# Fix: https://github.com/koalaman/shellcheck/wiki/SC3014 +SHELL ["/bin/bash", "-o", "pipefail", "-c"] + +USER root + +RUN apt update \ + && apt install --yes --quiet --no-install-recommends \ + libmagic-dev \ + && rm -rf /var/lib/apt/lists/* + + +# Switch back to jovyan to avoid accidental container runs as root +USER ${NB_UID} +WORKDIR "${HOME}" + +COPY --from=ghcr.io/astral-sh/uv:0.4 /uv /bin/uv + +RUN --mount=type=cache,target=/root/.cache/uv \ + --mount=type=bind,source=uv.lock,target=uv.lock \ + --mount=type=bind,source=pyproject.toml,target=pyproject.toml \ + uv export --extra plugins | uv pip install -r /dev/stdin --system + + +# Get rid ot the following message when you open a terminal in jupyterlab: +# groups: cannot find name for group ID 11320 +RUN touch ${HOME}/.hushlogin diff --git a/configs/nginx.conf b/configs/nginx.conf new file mode 100644 index 0000000..1b8531f --- /dev/null +++ b/configs/nginx.conf @@ -0,0 +1,82 @@ +map $http_upgrade $connection_upgrade { + default upgrade; + '' close; +} + +server { + listen 80; + server_name localhost; + proxy_set_header Host $host; + + gzip_min_length 1000; + gzip_buffers 4 8k; + gzip_http_version 1.0; + gzip_disable "msie6"; + gzip_vary on; + gzip on; + gzip_proxied any; + gzip_types + text/css + text/javascript + text/xml + text/plain + application/javascript + application/x-javascript + application/json; + + location / { + proxy_pass http://app:8000; + } + + location ~ /nomad-oasis\/?(gui)?$ { + rewrite ^ /nomad-oasis/gui/ permanent; + } + + location /nomad-oasis/gui/ { + proxy_intercept_errors on; + error_page 404 = @redirect_to_index; + proxy_pass http://app:8000; + } + + location @redirect_to_index { + rewrite ^ /nomad-oasis/gui/index.html break; + proxy_pass http://app:8000; + } + + location ~ \/gui\/(service-worker\.js|meta\.json)$ { + add_header Last-Modified $date_gmt; + add_header Cache-Control 'no-store, no-cache, must-revalidate, proxy-revalidate, max-age=0'; + if_modified_since off; + expires off; + etag off; + proxy_pass http://app:8000; + } + + location ~ /api/v1/uploads(/?$|.*/raw|.*/bundle?$) { + client_max_body_size 35g; + proxy_request_buffering off; + proxy_pass http://app:8000; + } + + location ~ /api/v1/.*/download { + proxy_buffering off; + proxy_pass http://app:8000; + } + + location /nomad-oasis/north/ { + client_max_body_size 500m; + proxy_pass http://north:9000; + + proxy_set_header X-Real-IP $remote_addr; + proxy_set_header Host $host; + proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; + + # websocket headers + proxy_http_version 1.1; + proxy_set_header Upgrade $http_upgrade; + proxy_set_header Connection $connection_upgrade; + proxy_set_header X-Scheme $scheme; + + proxy_buffering off; + } +} diff --git a/configs/nomad.yaml b/configs/nomad.yaml new file mode 100644 index 0000000..b23f063 --- /dev/null +++ b/configs/nomad.yaml @@ -0,0 +1,29 @@ +services: + api_host: "localhost" + api_base_path: "/nomad-oasis" + +oasis: + is_oasis: true + uses_central_user_management: true + +north: + jupyterhub_crypt_key: "978bfb2e13a8448a253c629d8dd84ff89587f30e635b753153960930cad9d36d" + tools: + options: + jupyter: + image: ghcr.io/fairmat-nfdi/nomad-distribution-template/jupyter:main + +meta: + deployment: "oasis" + deployment_url: "https://my-oasis.org/api" + maintainer_email: "me@my-oasis.org" + +logstash: + enable: false + +mongo: + db_name: nomad_oasis_v1 + +elastic: + entries_index: nomad_oasis_entries_v1 + materials_index: nomad_oasis_materials_v1 diff --git a/docker-compose.yaml b/docker-compose.yaml index 8483e50..e966e3f 100644 --- a/docker-compose.yaml +++ b/docker-compose.yaml @@ -1,5 +1,3 @@ -version: "3" - services: # broker for celery rabbitmq: @@ -70,7 +68,7 @@ services: # nomad worker (processing) worker: restart: unless-stopped - image: ghcr.io/fairmat-nfdi/nomad-distribution-template:main + image: ghcr.io/fairmat-nfdi/nomad-distribution-template/app:main container_name: nomad_oasis_worker environment: NOMAD_SERVICE: nomad_oasis_worker @@ -93,7 +91,7 @@ services: # nomad app (api + proxy) app: restart: unless-stopped - image: ghcr.io/fairmat-nfdi/nomad-distribution-template:main + image: ghcr.io/fairmat-nfdi/nomad-distribution-template/app:main container_name: nomad_oasis_app environment: NOMAD_SERVICE: nomad_oasis_app @@ -132,7 +130,7 @@ services: # nomad remote tools hub (JupyterHUB, e.g. for AI Toolkit) north: restart: unless-stopped - image: ghcr.io/fairmat-nfdi/nomad-distribution-template:main + image: ghcr.io/fairmat-nfdi/nomad-distribution-template/app:main container_name: nomad_oasis_north environment: NOMAD_SERVICE: nomad_oasis_north @@ -149,7 +147,7 @@ services: # - ./configs/nomad.yaml:/app/nomad.yaml - ./.volumes/fs:/app/.volumes/fs - /var/run/docker.sock:/var/run/docker.sock - user: '1000:991' + user: "1000:991" command: python -m nomad.cli admin run hub healthcheck: test: @@ -167,7 +165,7 @@ services: # to enable the logtransfer service run "docker compose --profile with_logtransfer up" logtransfer: restart: unless-stopped - image: ghcr.io/fairmat-nfdi/nomad-distribution-template:main + image: ghcr.io/fairmat-nfdi/nomad-distribution-template/app:main container_name: nomad_oasis_logtransfer environment: NOMAD_SERVICE: nomad_oasis_logtransfer diff --git a/nomad-oasis.zip b/nomad-oasis.zip deleted file mode 100644 index 6ae5518441e7af952edc2b2880c6681872a1207a..0000000000000000000000000000000000000000 GIT binary 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No newline at end of file diff --git a/plugins.txt b/plugins.txt deleted file mode 100644 index 041a1f0..0000000 --- a/plugins.txt +++ /dev/null @@ -1,2 +0,0 @@ -nomad-measurements -nomad-material-processing diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..d884a7e --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,52 @@ +[build-system] +requires = ["setuptools>=64"] +build-backend = "setuptools.build_meta" + +[project] +classifiers = [ + "Intended Audience :: Developers", + "Operating System :: OS Independent", + "Programming Language :: Python", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", +] +name = "nomad-distribution" +description = "nomad distribution template" +version = "0.1" +readme = "README.md" +requires-python = ">=3.9" +license = { file = "LICENSE" } +dependencies = ["nomad-lab[parsing, infrastructure]>=1.3.4"] + +[project.optional-dependencies] +plugins = [ + "perovskite-solar-cell-database @ git+https://github.com/FAIRmat-NFDI/nomad-perovskite-solar-cells-database.git@f394d21abafeb659729af0c94e5f90949fce01c1", + "nomad-porous-materials @ git+https://github.com/FAIRmat-NFDI/nomad-porous-materials.git@522f4a3208077f534f1c5e886527ee2104283d0b", + "nomad-aitoolkit @ git+https://github.com/FAIRmat-NFDI/nomad-aitoolkit.git@b203f8eb28dc4b6771a39d5c5b7ad3d9d8583ac8", + "nomad-simulations==0.0.1", + "pynxtools[convert]==0.5.0", + "nomad-schema-plugin-run>=1.0.1", + "nomad-schema-plugin-simulation-workflow>=1.0.1", + "nomad-normalizer-plugin-bandstructure>=1.0", + "nomad-normalizer-plugin-dos>=1.0", + "nomad-normalizer-plugin-soap>=1.0", + "nomad-normalizer-plugin-spectra>=1.0", + "nomad-normalizer-plugin-system>=1.0", + "nomad-normalizer-plugin-simulation-workflow>=1.0", + "eelsdbconverter @ git+https://github.com/nomad-coe/nomad-parser-eelsdb.git@entry-point", + "nomad-parser-plugins-electronic>=1.0", + "nomad-parser-plugins-atomistic>=1.0", + "nomad-parser-plugins-workflow>=1.0", + "nomad-parser-plugins-database>=1.0", +] +dev = ["nomad-lab[parsing, infrastructure, dev]>=1.3.4"] + +[tool.uv] +extra-index-url = [ + "https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple", +] +constraint-dependencies = ["hyperspy>=1.7.6"] + +[tool.setuptools.packages.find] +exclude = ["gui*", "docs*", "config*"] diff --git a/scripts/run-worker.sh b/scripts/run-worker.sh new file mode 100755 index 0000000..57ce33e --- /dev/null +++ b/scripts/run-worker.sh @@ -0,0 +1,3 @@ +#!/bin/bash + +python -m celery -A nomad.processing worker -B -l info -Q celery diff --git a/scripts/run.sh b/scripts/run.sh new file mode 100755 index 0000000..ca99a7c --- /dev/null +++ b/scripts/run.sh @@ -0,0 +1,3 @@ +#!/bin/bash + +python -m nomad.cli admin run app --with-gui --gunicorn --host 0.0.0.0 $@ diff --git a/template_README.md b/template_README.md index d43d936..3bf2422 100644 --- a/template_README.md +++ b/template_README.md @@ -2,16 +2,16 @@ # GITHUB_REPOSITORY_OWNER's NOMAD Oasis Distribution -This is the NOMAD Oasis distribution of GITHUB_REPOSITORY_OWNER. +This is the NOMAD Oasis distribution of GITHUB_REPOSITORY_OWNER. Below are instructions for how to [deploy this distribution](#deploying-the-distribution) and how to customize it through [adding plugins](#adding-a-plugin). -> [!IMPORTANT] +> [!IMPORTANT] > Depending on the settings of the owner of this repository, the distributed image might > be private and require authentication to pull. > If you want to keep the image private you need to configure and use a personal access > token (PAT) according to the instructions in the GitHub docs [here](https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-container-registry#authenticating-with-a-personal-access-token-classic). -> If you want to make the image public (recommended), you should make sure that your +> If you want to make the image public (recommended), you should make sure that your > organization settings allow public packages and make this package public after building it. > You can read more about this in the GitHub docs [here](https://docs.github.com/en/packages/learn-github-packages/configuring-a-packages-access-control-and-visibility). @@ -28,43 +28,62 @@ Below are instructions for how to deploy this NOMAD Oasis distribution ### For a new Oasis 1. Make sure you have [docker](https://docs.docker.com/engine/install/) installed. -Docker nowadays comes with `docker compose` built in. Prior, you needed to -install the stand-alone [docker-compose](https://docs.docker.com/compose/install/). -2. Get the `nomad-oasis.zip` archive from your distribution repository using for example curl + Docker nowadays comes with `docker compose` built in. Prior, you needed to + install the stand-alone [docker-compose](https://docs.docker.com/compose/install/). + +2. Clone the repository or download the repository as a zip file. + ```sh -curl -L -o nomad-oasis.zip "https://github.com/GITHUB_REPOSITORY/raw/main/nomad-oasis.zip" +git clone https://github.com/GITHUB_REPOSITORY.git +cd GITHUB_REPOSITORY_NAME ``` -3. Unzip the `nomad-oasis.zip` file and enter the extracted directory + +or + ```sh -unzip nomad-oasis.zip -cd nomad-oasis +curl-L -o GITHUB_REPOSITORY_NAME.zip "https://github.com/GITHUB_REPOSITORY/archive/main.zip" +unzip GITHUB_REPOSITORY_NAME.zip +cd GITHUB_REPOSITORY_NAME ``` -4. _On Linux only,_ recursively change the owner of the `.volumes` directory to the nomad user (1000) + +3. _On Linux only,_ recursively change the owner of the `.volumes` directory to the nomad user (1000) + ```sh sudo chown -R 1000 .volumes ``` -5. Pull the images specified in the `docker-compose.yaml` (retrieved from the `nomad-oasis.zip`). + +4. Pull the images specified in the `docker-compose.yaml` + Note that the image needs to be public or you need to provide a PAT (see "Important" note above). + ```sh docker compose pull ``` -6. And run it with docker compose in detached (--detach or -d) mode + +5. And run it with docker compose in detached (--detach or -d) mode + ```sh docker compose up -d ``` -7. Optionally you can now test that NOMAD is running with + +6. Optionally you can now test that NOMAD is running with + ``` curl localhost/nomad-oasis/alive ``` -8. Finally, open [http://localhost/nomad-oasis](http://localhost/nomad-oasis) in your browser to start using your new NOMAD Oasis. + +7. Finally, open [http://localhost/nomad-oasis](http://localhost/nomad-oasis) in your browser to start using your new NOMAD Oasis. Whenever you update your image you need to shut down NOMAD using + ```sh docker compose down ``` -and then repeat steps 5. and 6. above. + +and then repeat steps 4. and 5. above. #### NOMAD Remote Tools Hub (NORTH) + To run NORTH (the NOMAD Remote Tools Hub), the `hub` container needs to run docker and the container has to be run under the docker group. You need to replace the default group id `991` in the `docker-compose.yaml`'s `hub` section with your systems docker group id. @@ -85,54 +104,61 @@ the inclusion of the `nomad.yaml` under the volumes key of those services in the `docker-compose.yaml`. ```yaml - volumes: - # - ./configs/nomad.yaml:/app/nomad.yaml +volumes: + # - ./configs/nomad.yaml:/app/nomad.yaml ``` To run the new image you can follow steps 5. and 6. [above](#for-a-new-oasis). ## Adding a plugin -To add a new plugin to the docker image you should add it to the [plugins.txt](plugins.txt) file. +To add a new plugin to the docker image you should add it to the plugins table in the `pyproject.toml` file. Here you can put either plugins distributed to PyPI, e.g. + ``` nomad-material-processing ``` + or plugins in a git repository with either the commit hash + ``` -git+https://github.com/FAIRmat-NFDI/nomad-measurements.git@71b7e8c9bb376ce9e8610aba9a20be0b5bce6775 +"nomad-measurements @ git+https://github.com/FAIRmat-NFDI/nomad-measurements.git@71b7e8c9bb376ce9e8610aba9a20be0b5bce6775" ``` + or with a tag + ``` -git+https://github.com/FAIRmat-NFDI/nomad-measurements.git@v0.0.4 +"nomad-measurements @ git+https://github.com/FAIRmat-NFDI/nomad-measurements.git@v0.0.4" ``` + To add a plugin in a subdirectory of a git repository you can use the `subdirectory` option, e.g. + ``` -git+https://github.com/FAIRmat-NFDI/AreaA-data_modeling_and_schemas.git@30fc90843428d1b36a1d222874803abae8b1cb42#subdirectory=PVD/PLD/jeremy_ikz/ikz_pld_plugin +"ikz_pld_plugin @ git+https://github.com/FAIRmat-NFDI/AreaA-data_modeling_and_schemas.git@30fc90843428d1b36a1d222874803abae8b1cb42#subdirectory=PVD/PLD/jeremy_ikz/ikz_pld_plugin" ``` If the plugin is new, you also need to add it under `plugins` in the [nomad.yaml](nomad.yaml) config file that will be included in the image. -For example, if you have added a schema plugin `nomad_material_processing` you should add +For example, if you have added a schema plugin `legacy_plugin` you should add the following: ```yaml plugins: options: - schemas/nomad_material_processing: - python_package: nomad_material_processing + schemas/legacy_plugin: + python_package: legacy_plugin ``` -Once the changes have been committed to the main branch, the new image will automatically +Once the changes have been committed to the main branch, the new image will automatically be generated. ## FAQ/Trouble shooting - *I get an* `Error response from daemon: Head "https://ghcr.io/v2/GITHUB_REPOSITORY/manifests/main": unauthorized` - *when trying to pull my docker image.* - - Most likely you have not made the package public or provided a personal access token (PAT). - You can read how to make your package public in the GitHub docs [here](https://docs.github.com/en/packages/learn-github-packages/configuring-a-packages-access-control-and-visibility) - or how to configure a PAT (if you want to keep the distribution private) in the GitHub - docs [here](https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-container-registry#authenticating-with-a-personal-access-token-classic). +_I get an_ `Error response from daemon: Head "https://ghcr.io/v2/GITHUB_REPOSITORY/manifests/main": unauthorized` +_when trying to pull my docker image._ + +Most likely you have not made the package public or provided a personal access token (PAT). +You can read how to make your package public in the GitHub docs [here](https://docs.github.com/en/packages/learn-github-packages/configuring-a-packages-access-control-and-visibility) +or how to configure a PAT (if you want to keep the distribution private) in the GitHub +docs [here](https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-container-registry#authenticating-with-a-personal-access-token-classic). diff --git a/uv.lock b/uv.lock new file mode 100644 index 0000000..e01ec44 --- /dev/null +++ b/uv.lock @@ -0,0 +1,7498 @@ +version = 1 +requires-python = ">=3.9" +resolution-markers = [ + "python_full_version < '3.11' and platform_system == 'Windows'", + "python_full_version < '3.11' and platform_system != 'Windows'", + "python_full_version == '3.11.*'", + "python_full_version >= '3.12'", +] + +[manifest] +constraints = [{ name = "hyperspy", specifier = ">=1.7.6" }] + +[[package]] +name = "aiosmtpd" +version = "1.4.6" +source = { registry = 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