diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml new file mode 100644 index 0000000..ea857fd --- /dev/null +++ b/.github/workflows/cd.yml @@ -0,0 +1,21 @@ +name: cd + +on: + push: + branches-ignore: + - main + +jobs: + deploy: + if: "!contains(github.event.head_commit.message, 'skipci')" + uses: octue/workflows/.github/workflows/deploy-cloud-run-service.yml@main + permissions: + id-token: write + contents: read + with: + gcp_project_name: octue-twined-services + gcp_project_number: 13074362726 + gcp_region: europe-west9 + gcp_resource_affix: octue + gcp_service_name: turbsim-service + local_dockerfile: ./Dockerfile diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml new file mode 100644 index 0000000..f9e0505 --- /dev/null +++ b/.github/workflows/codeql.yml @@ -0,0 +1,70 @@ +# For most projects, this workflow file will not need changing; you simply need +# to commit it to your repository. +# +# You may wish to alter this file to override the set of languages analyzed, +# or to provide custom queries or build logic. +# +# ******** NOTE ******** +# We have attempted to detect the languages in your repository. Please check +# the `language` matrix defined below to confirm you have the correct set of +# supported CodeQL languages. +# +name: "CodeQL" + +on: + push: + branches: ["main"] + +jobs: + analyze: + name: Analyze + runs-on: ubuntu-latest + permissions: + actions: read + contents: read + security-events: write + + strategy: + fail-fast: false + matrix: + language: ["python"] + # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ] + # Use only 'java' to analyze code written in Java, Kotlin or both + # Use only 'javascript' to analyze code written in JavaScript, TypeScript or both + # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support + + steps: + - name: Checkout repository + uses: actions/checkout@v3 + + # Initializes the CodeQL tools for scanning. + - name: Initialize CodeQL + uses: github/codeql-action/init@v2 + with: + languages: ${{ matrix.language }} + # If you wish to specify custom queries, you can do so here or in a config file. + # By default, queries listed here will override any specified in a config file. + # Prefix the list here with "+" to use these queries and those in the config file. + + # Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs + # queries: security-extended,security-and-quality + + # Autobuild attempts to build any compiled languages (C/C++, C#, Go, or Java). + # If this step fails, then you should remove it and run the build manually (see below) + - name: Autobuild + uses: github/codeql-action/autobuild@v2 + + # ℹī¸ Command-line programs to run using the OS shell. + # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun + + # If the Autobuild fails above, remove it and uncomment the following three lines. + # modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance. + + # - run: | + # echo "Run, Build Application using script" + # ./location_of_script_within_repo/buildscript.sh + + - name: Perform CodeQL Analysis + uses: github/codeql-action/analyze@v2 + with: + category: "/language:${{matrix.language}}" diff --git a/.github/workflows/python-ci.yml b/.github/workflows/python-ci.yml index a254a30..e3bab68 100644 --- a/.github/workflows/python-ci.yml +++ b/.github/workflows/python-ci.yml @@ -1,3 +1,5 @@ +# This workflow will install the Python dependencies and run the tests. + name: python-ci on: @@ -7,20 +9,35 @@ on: jobs: check-semantic-version: + if: "!contains(github.event.head_commit.message, 'skipci')" + uses: octue/workflows/.github/workflows/check-semantic-version.yml@main + with: + path: pyproject.toml + breaking_change_indicated_by: minor + + + test: if: "!contains(github.event.head_commit.message, 'skipci')" runs-on: ubuntu-latest + permissions: + contents: 'read' + id-token: 'write' steps: - - uses: actions/checkout@v3 + - name: Checkout Repository + uses: actions/checkout@v4 + + - name: Install Poetry + uses: snok/install-poetry@v1 + + - name: Install package + run: poetry install + + - name: Authenticate with Google Cloud + id: auth + uses: google-github-actions/auth@v2 with: - # Set fetch-depth to 0 to fetch all tags (necessary for git-mkver to determine the correct semantic version). - fetch-depth: 0 - - uses: actions/setup-python@v2 - - name: Install git-mkver - run: | - curl -L https://github.com/idc101/git-mkver/releases/download/v1.2.1/git-mkver-linux-amd64-1.2.1.tar.gz \ - | tar xvz \ - && sudo mv git-mkver /usr/local/bin - - name: Install semantic version checker - run: pip install git+https://github.com/octue/conventional-commits - - name: Check version - run: check-semantic-version setup.py + workload_identity_provider: "projects/13074362726/locations/global/workloadIdentityPools/github-actions-pool/providers/github-actions-provider" + service_account: "github-actions@octue-twined-services.iam.gserviceaccount.com" + + - name: Run tests + run: poetry run python -m unittest diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 5a5d177..834636c 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -1,5 +1,3 @@ -# This workflow releases a new version of the package. - name: Release # Only trigger when a pull request into main branch is merged. @@ -9,14 +7,49 @@ on: branches: - main + jobs: + test: + runs-on: ubuntu-latest + permissions: + contents: 'read' + id-token: 'write' + steps: + - name: Checkout Repository + uses: actions/checkout@v4 + + - name: Install Poetry + uses: snok/install-poetry@v1 + + - name: Install package + run: poetry install + + - name: Authenticate with Google Cloud + id: auth + uses: google-github-actions/auth@v2 + with: + workload_identity_provider: "projects/13074362726/locations/global/workloadIdentityPools/github-actions-pool/providers/github-actions-provider" + service_account: "github-actions@octue-twined-services.iam.gserviceaccount.com" + + - name: Run tests + run: poetry run python -m unittest + + release: + if: "github.event.pull_request.merged == true" + needs: test runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 + + - name: Install Poetry + uses: snok/install-poetry@v1 + + - name: Check pyproject.toml file + run: poetry check - name: Get package version - run: echo "PACKAGE_VERSION=$(python setup.py --version)" >> $GITHUB_ENV + run: echo "PACKAGE_VERSION=$(poetry version -s)" >> $GITHUB_ENV - name: Create Release uses: actions/create-release@v1 @@ -28,3 +61,18 @@ jobs: body: ${{ github.event.pull_request.body }} draft: false prerelease: false + + + deploy: + uses: octue/workflows/.github/workflows/build-twined-service.yml@0.4.2 + needs: release + permissions: + id-token: write + contents: read + with: + gcp_project_name: octue-twined-services + gcp_project_number: 13074362726 + gcp_region: europe-west9 + gcp_resource_affix: octue + gcp_service_name: turbsim-service + local_dockerfile: ./Dockerfile diff --git a/.github/workflows/update-pull-request.yml b/.github/workflows/update-pull-request.yml index 3586423..13a893e 100644 --- a/.github/workflows/update-pull-request.yml +++ b/.github/workflows/update-pull-request.yml @@ -1,35 +1,18 @@ # This workflow updates the pull request description with an auto-generated section containing the categorised commit -# message headers of the commits since the last pull request merged into main. The auto generated section is enveloped -# between two comments: "" and "". Anything -# outside these in the description is left untouched. Auto-generated updates can be skipped for a commit if +# message headers of the pull request's commits. The auto generated section is enveloped between two comments: +# "" and "". Anything outside these in the +# description is left untouched. Auto-generated updates can be skipped for a commit if # "" is added to the pull request description. name: update-pull-request -# Only trigger for pull requests into main branch. -on: - pull_request: - branches: - - main +on: pull_request jobs: description: - if: "!contains(github.event.pull_request.body, '')" - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v3 - with: - # Set fetch-depth to 0 to fetch all commit history (necessary for compiling pull request description). - fetch-depth: 0 - - name: Install release note compiler - run: pip install git+https://github.com/octue/conventional-commits - - name: Compile new pull request description - run: | - echo 'PULL_REQUEST_NOTES<> $GITHUB_ENV - echo "$(compile-release-notes PULL_REQUEST_START --pull-request-url=${{ github.event.pull_request.url }} --api-token=${{ secrets.GITHUB_TOKEN }})" >> $GITHUB_ENV - echo EOF >> $GITHUB_ENV - - name: Update pull request body - uses: riskledger/update-pr-description@v2 - with: - body: ${{ env.PULL_REQUEST_NOTES }} - token: ${{ secrets.GITHUB_TOKEN }} + uses: octue/workflows/.github/workflows/generate-pull-request-description.yml@main + secrets: + token: ${{ secrets.GITHUB_TOKEN }} + permissions: + contents: read + pull-requests: write diff --git a/.gitignore b/.gitignore index 872c981..e7ec72b 100644 --- a/.gitignore +++ b/.gitignore @@ -129,3 +129,4 @@ dmypy.json .pyre/ .idea +.DS_store diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index d97bf04..689ac44 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -12,22 +12,19 @@ repos: - id: check-yaml - id: check-added-large-files - - repo: https://github.com/PyCQA/isort - rev: 5.9.3 + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.9.4 hooks: - - id: isort + - id: ruff + name: Ruff lint + args: [--fix, --exit-non-zero-on-fix] - - repo: https://github.com/psf/black - rev: 21.9b0 - hooks: - - id: black - args: ['--line-length', '120'] + - id: ruff + name: Ruff isort + args: [check, --select, I, --fix] - - repo: https://gitlab.com/pycqa/flake8 - rev: 3.9.2 - hooks: - - id: flake8 - language_version: python3 + - id: ruff-format + name: Ruff format - repo: https://github.com/windpioneers/pre-commit-hooks rev: 0.0.5 @@ -35,19 +32,10 @@ repos: - id: check-branch-name args: - '^main$' - - '^development$' - - '^devops/([a-z][a-z0-9]*)(-[a-z0-9]+)*$' - - '^doc/([a-z][a-z0-9]*)(-[a-z0-9]+)*$' - - '^feature/([a-z][a-z0-9]*)(-[a-z0-9]+)*$' - - '^enhancement/([a-z][a-z0-9]*)(-[a-z0-9]+)*$' - - '^fix/([a-z][a-z0-9]*)(-[a-z0-9]+)*$' - - '^hotfix/([a-z][a-z0-9]*)(-[a-z0-9]+)*$' - - '^review/([a-z][a-z0-9]*)(-[a-z0-9]+)*$' - - '^refactor/([a-z][a-z0-9]*)(-[a-z0-9]+)*$' - - '^test/([a-z][a-z0-9]*)(-[a-z0-9]+)*$' + - "^([a-z][a-z0-9]*)(-[a-z0-9]+)*$" - repo: https://github.com/octue/conventional-commits - rev: 0.5.3 + rev: 0.9.0 hooks: - id: check-commit-message-is-conventional stages: [commit-msg] diff --git a/ATTRIBUTION.md b/ATTRIBUTION.md new file mode 100644 index 0000000..08926ab --- /dev/null +++ b/ATTRIBUTION.md @@ -0,0 +1,26 @@ +# ATTRIBUTION + +In addition to some modules of our own, `octue/turbsim-service` is based on a collection of other projects that we've +drawn together, patched, enhanced and documented. + +The nature of OSS is to stand on the shoulders of giants, and we owe them a ton... here are their licenses: + +## `aerosense-ai/turbsim-service` + +
+ Show license + + +# turbsim-service + +Copyright (c) 2020-2022 The Aerosense Research Partners + +Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: + +Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. +Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. +All advertising materials mentioning features or use of this software must display the following acknowledgement: This product includes software developed by the The Aerosense Research Partners. +Neither the name of the The Aerosense Research Partners nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. +THIS SOFTWARE IS PROVIDED BY The Aerosense Research Partners AS IS AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL The Aerosense Research Partners BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +
diff --git a/Dockerfile b/Dockerfile index 18fc4ce..c516c10 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,26 +1,34 @@ -FROM octue/openfast:3.1.0 +FROM ghcr.io/openfast/openfast:3.5.3 # Allow statements and log messages to immediately appear in the Knative logs on Google Cloud. ENV PYTHONUNBUFFERED True -ENV PROJECT_ROOT=/app +ENV PROJECT_ROOT=/workspace WORKDIR $PROJECT_ROOT -COPY setup.py setup.py -COPY . . +RUN apt-get update -y && apt-get install -y --fix-missing curl python3.11 && rm -rf /var/lib/apt/lists/* -RUN pip3 install -e . +# Install poetry. +ENV POETRY_HOME=/root/.poetry +ENV PATH "$POETRY_HOME/bin:$PATH" +RUN curl -sSL https://install.python-poetry.org | python3.11 - && poetry config virtualenvs.create false; -EXPOSE $PORT +# Copy in dependency files for caching. +COPY pyproject.toml poetry.lock ./ -ENV USE_OCTUE_LOG_HANDLER=1 -ENV COMPUTE_PROVIDER=GOOGLE_CLOUD_RUN +# Install just the dependencies to utilise layer caching for quick rebuilds. +RUN poetry install \ + --no-ansi \ + --no-interaction \ + --no-cache \ + --no-root \ + --only main -ARG GUNICORN_WORKERS=1 -ENV GUNICORN_WORKERS=$GUNICORN_WORKERS +COPY . . -ARG GUNICORN_THREADS=8 -ENV GUNICORN_THREADS=$GUNICORN_THREADS +# Install local packages. +RUN poetry install --only main -# Timeout is set to 0 to disable the timeouts of the workers to allow Cloud Run to handle instance scaling. -CMD exec gunicorn --bind :$PORT --workers $GUNICORN_WORKERS --threads $GUNICORN_THREADS --timeout 0 octue.cloud.deployment.google.cloud_run.flask_app:app +ENV USE_OCTUE_LOG_HANDLER=1 +ENV COMPUTE_PROVIDER=GOOGLE_KUEUE +CMD ["octue", "question", "ask", "local"] diff --git a/LICENSE b/LICENSE index 63bd9cd..584e948 100644 --- a/LICENSE +++ b/LICENSE @@ -1,11 +1,21 @@ -# turbsim-service +MIT License -Copyright (c) 2020-2022 The Aerosense Research Partners +Copyright (c) 2024 Octue -Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: -Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. -Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. -All advertising materials mentioning features or use of this software must display the following acknowledgement: This product includes software developed by the The Aerosense Research Partners. -Neither the name of the The Aerosense Research Partners nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. -THIS SOFTWARE IS PROVIDED BY The Aerosense Research Partners AS IS AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL The Aerosense Research Partners BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/README.md b/README.md new file mode 100644 index 0000000..34462f5 --- /dev/null +++ b/README.md @@ -0,0 +1 @@ +# Octue Turbsim Service diff --git a/app.py b/app.py deleted file mode 100644 index 1d51599..0000000 --- a/app.py +++ /dev/null @@ -1,50 +0,0 @@ -import datetime -import logging -import os -import tempfile - -from octue.resources import Datafile, Dataset -from octue.utils.threads import run_logged_subprocess - - -logger = logging.getLogger(__name__) - - -OUTPUT_EXTENSION = ".bts" -OUTPUT_FILENAME = "TurbSim" + OUTPUT_EXTENSION - - -def run(analysis): - """Run a turbsim analysis on the input file specified in the input manifest, writing the output file to the cloud. - - :param octue.resources.Analysis analysis: - :return None: - """ - start_datetime = datetime.datetime.now() - - with tempfile.TemporaryDirectory() as temporary_directory: - input_dataset = analysis.input_manifest.datasets["turbsim"] - input_dataset.download(temporary_directory) - input_file = input_dataset.files.one() - - logger.info("Starting turbsim analysis.") - run_logged_subprocess(command=["turbsim", input_file.local_path], logger=logger) - - old_output_filename = os.path.splitext(input_file.local_path)[0] + OUTPUT_EXTENSION - - with tempfile.TemporaryDirectory() as new_temporary_directory: - new_output_filename = os.path.join(new_temporary_directory, OUTPUT_FILENAME) - os.rename(old_output_filename, new_output_filename) - - # Instantiate a datafile for the output file. - with Datafile(path=new_output_filename, mode="a") as (datafile, f): - datafile.timestamp = start_datetime - datafile.labels = ["turbsim", "output"] - - analysis.output_manifest.datasets["turbsim"] = Dataset(name="turbsim", path=new_temporary_directory) - - # Explicitly call `finalise` here instead of relying on implicit finalisation so the temporary directory - # still exists when it's called. - analysis.finalise() - - logger.info("Finished turbsim analysis.") diff --git a/app_configuration.json b/app_configuration.json index 0eecb10..ff111f3 100644 --- a/app_configuration.json +++ b/app_configuration.json @@ -1,3 +1,3 @@ { - "output_location": "gs://openfast-data/output" + "output_location": "gs://octue-octue-twined-services-octue-twined/turbsim-service/outputs" } diff --git a/mkver.conf b/mkver.conf deleted file mode 100644 index 0370c28..0000000 --- a/mkver.conf +++ /dev/null @@ -1,41 +0,0 @@ -tagPrefix: "" -defaults { - tag: false - tagMessageFormat: "Release/{Tag}" - preReleaseFormat: "RC{PreReleaseNumber}" - buildMetaDataFormat: "{Branch}.{ShortHash}" - includeBuildMetaData: false - whenNoValidCommitMessages: IncrementPatch - patches: [setup.py] -} - -patches: [ - { - name: setup.py - filePatterns: ["setup.py"] - replacements: [ - { - find: "version=\"{VersionRegex}\"" - replace: "version=\"{Version}\"" - } - ] - } -] - -commitMessageActions: [ - # Disable major version increments while package is still in beta (i.e. keep the version below 1.0.0). - { - pattern: "BREAKING CHANGE" - action: IncrementMinor - } - { - pattern: "BREAKING-CHANGE" - action: IncrementMinor - } - - # All new features require a minor version increase. - { - pattern: "FEA:" - action: IncrementMinor - } -] diff --git a/octue.yaml b/octue.yaml index 16e9bc0..c047bbf 100644 --- a/octue.yaml +++ b/octue.yaml @@ -1,12 +1,10 @@ services: - - name: turbsim-service - organisation: aerosense + - namespace: octue + name: turbsim-service + app_source_path: turbsim_service app_configuration_path: app_configuration.json - project_name: aerosense-twined - region: europe-west1 - repository_owner: aerosense-ai - repository_name: turbsim-service - branch_pattern: ^main$ - dockerfile_path: Dockerfile - maximum_instances: 10 - memory: 1024Mi + diagnostics_cloud_path: gs://octue-octue-twined-services-octue-twined/turbsim-service/diagnostics + event_store_table_id: octue_twined.service-events + service_registries: + - name: Octue service registry + endpoint: https://europe-west9-octue-twined-services.cloudfunctions.net/main-octue-twined-service-registry diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..ffc515d --- /dev/null +++ b/poetry.lock @@ -0,0 +1,1632 @@ +# This file is automatically @generated by Poetry 2.1.1 and should not be changed by hand. + +[[package]] +name = "attrs" +version = "25.1.0" +description = "Classes Without Boilerplate" +optional = false +python-versions = ">=3.8" +groups = ["main"] +files = [ + {file = "attrs-25.1.0-py3-none-any.whl", hash = "sha256:c75a69e28a550a7e93789579c22aa26b0f5b83b75dc4e08fe092980051e1090a"}, + {file = "attrs-25.1.0.tar.gz", hash = "sha256:1c97078a80c814273a76b2a298a932eb681c87415c11dee0a6921de7f1b02c3e"}, +] + +[package.extras] +benchmark = ["cloudpickle ; 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Lugg "] +readme = "README.md" + +[tool.poetry.dependencies] +python = "^3.11" +octue = { git = "https://github.com/octue/octue-sdk-python", branch = "rc-kueue" } + +[tool.poetry.group.dev.dependencies] +pre-commit = "<=3" +coverage = "^7.3.2" + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" + +[tool.ruff] +line-length = 120 +# Enable pycodestyle (`E`) and Pyflakes (`F`) codes. +lint.select = ["E", "F"] +# Ignore E501 line-too-long - see https://docs.astral.sh/ruff/faq/#is-the-ruff-linter-compatible-with-black for why +lint.ignore = ["F405", "E501", "E203", "E731", "N818"] + +[tool.ruff.lint.isort] +known-first-party = ["octue", "app", "fractal", "test", "tests", "twined"] +section-order = ["future", "standard-library", "third-party", "first-party", "local-folder"] +force-sort-within-sections = true diff --git a/requirements-dev.txt b/requirements-dev.txt deleted file mode 100644 index ea90bb9..0000000 --- a/requirements-dev.txt +++ /dev/null @@ -1,8 +0,0 @@ -# Quality control -pre-commit<=3 - -# Testing -coverage - -# Install the current app (as editable, so you can develop on it) ---editable . diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index c02a95d..0000000 --- a/setup.cfg +++ /dev/null @@ -1,23 +0,0 @@ -[metadata] -long_description = file: README.md -long_description_content_type = text/markdown; charset=UTF-8 - -[flake8] -max-line-length = 120 -exclude = .tox,.git,*/migrations/*,*/static/CACHE/*,docs,node_modules,build -ignore = F405, E501, W503, E203, E731 - -[isort] -line_length=120 -default_section = THIRDPARTY -known_third_party = requests, click, jsonschema -known_first_party = turbsim, tests -sections = FUTURE,STDLIB,THIRDPARTY,FIRSTPARTY,LOCALFOLDER -lines_after_imports=2 -# These are necessary for `isort` to create import statements that are -# compatible with `black`. Changing these will break auto-formatting. -# See . -multi_line_output=3 -include_trailing_comma=True -force_grid_wrap=0 -combine_as_imports=True diff --git a/setup.py b/setup.py deleted file mode 100644 index b4dcf8d..0000000 --- a/setup.py +++ /dev/null @@ -1,13 +0,0 @@ -from setuptools import setup - - -setup( - name="turbsim-service", - version="0.1.1", - author="cortadocodes ", - py_modules=["app"], - install_requires=[ - "coolname>=1.1,<2", - "octue==0.35.1", - ], -) diff --git a/tests/test_app.py b/tests/test_app.py index c16f8c0..c7c36c6 100644 --- a/tests/test_app.py +++ b/tests/test_app.py @@ -1,33 +1,115 @@ -import json import os +import tempfile import unittest from unittest.mock import patch from octue import Runner -from octue.cloud import storage +from octue.configuration import load_service_and_app_configuration from octue.log_handlers import apply_log_handler from octue.resources import Dataset, Manifest - apply_log_handler() REPOSITORY_ROOT = os.path.dirname(os.path.dirname(__file__)) -TWINE_PATH = os.path.join(REPOSITORY_ROOT, "twine.json") - -with open(os.path.join(REPOSITORY_ROOT, "app_configuration.json")) as f: - OUTPUT_LOCATION = storage.path.join(json.load(f)["output_location"], "testing", "turbsim") +BUCKET_NAME = "octue-octue-twined-services-octue-twined" +PROJECT_NAME = "octue-twined-services" class TestApp(unittest.TestCase): - def test_app(self): - """Test that the app takes input and produces an output manifest with a dataset containing a single `.bts` file.""" - runner = Runner(app_src=REPOSITORY_ROOT, twine=TWINE_PATH, output_location=OUTPUT_LOCATION) + def test_error_raised_if_input_dataset_empty(self): + """Test that an error is raised if the input dataset is empty.""" + with tempfile.TemporaryDirectory() as temporary_directory: + service_configuration, app_configuration = load_service_and_app_configuration( + service_configuration_path=os.path.join(REPOSITORY_ROOT, "octue.yaml") + ) + + runner = Runner.from_configuration( + service_configuration=service_configuration, + app_configuration=app_configuration, + project_name=PROJECT_NAME, + service_id="octue/turbsim-service:test", + ) + + input_manifest = Manifest(datasets={"turbsim": temporary_directory}) + + with self.assertRaises(ValueError): + runner.run(input_manifest=input_manifest.serialise()) + + def test_error_raised_if_input_dataset_has_more_than_two_files(self): + """Test that an error is raised if the input dataset has more than two files.""" + with tempfile.TemporaryDirectory() as temporary_directory: + for i in range(3): + with open(os.path.join(temporary_directory, f"file_{i}"), "w") as f: + f.write("Hello") + + service_configuration, app_configuration = load_service_and_app_configuration( + service_configuration_path=os.path.join(REPOSITORY_ROOT, "octue.yaml") + ) + + runner = Runner.from_configuration( + service_configuration=service_configuration, + app_configuration=app_configuration, + project_name=PROJECT_NAME, + service_id="octue/turbsim-service:test", + ) + + input_manifest = Manifest(datasets={"turbsim": temporary_directory}) + + with self.assertRaises(ValueError): + runner.run(input_manifest=input_manifest.serialise()) + + def test_with_turbsim_input_file_only(self): + """Test that the app works with a TurbSim input file only and produces an output manifest with a dataset + containing a single `.bts` file. + """ + service_configuration, app_configuration = load_service_and_app_configuration( + service_configuration_path=os.path.join(REPOSITORY_ROOT, "octue.yaml") + ) + + runner = Runner.from_configuration( + service_configuration=service_configuration, + app_configuration=app_configuration, + project_name=PROJECT_NAME, + service_id="octue/turbsim-service:test", + ) + + input_manifest = Manifest(datasets={"turbsim": f"gs://{BUCKET_NAME}/turbsim-service/testing/turbsim"}) + + # Mock running an OpenFAST analysis by creating an empty output file. + with patch("octue.utils.processes.run_logged_subprocess", self._create_mock_output_file): + analysis = runner.run(input_manifest=input_manifest.serialise()) + + self.assertIsNone(analysis.output_values) + self.assertIsNotNone(analysis.output_manifest) + self.assertTrue(len(analysis.output_manifest.datasets["turbsim"].files), 1) + + output_dataset = Dataset(path=analysis.output_manifest.datasets["turbsim"].path) + + with output_dataset.files.one() as (datafile, f): + self.assertEqual(f.read(), "This is a mock TurbSim output file.") + + def test_with_turbsim_input_file_and_profile_file(self): + """Test that the TurbSim service works when a profile file is provided alongside the input file.""" + service_configuration, app_configuration = load_service_and_app_configuration( + service_configuration_path=os.path.join(REPOSITORY_ROOT, "octue.yaml") + ) + + runner = Runner.from_configuration( + service_configuration=service_configuration, + app_configuration=app_configuration, + project_name=PROJECT_NAME, + service_id="octue/turbsim-service:test", + ) + + input_manifest = Manifest( + datasets={"turbsim": f"gs://{BUCKET_NAME}/turbsim-service/testing/turbsim_with_profile"} + ) - input_manifest = Manifest(datasets={"turbsim": "gs://openfast-data/testing/turbsim"}) + self.assertEqual(len(input_manifest.datasets["turbsim"].files), 2) # Mock running an OpenFAST analysis by creating an empty output file. - with patch("app.run_logged_subprocess", self._create_mock_output_file): + with patch("octue.utils.processes.run_logged_subprocess", self._create_mock_output_file): analysis = runner.run(input_manifest=input_manifest.serialise()) self.assertIsNone(analysis.output_values) diff --git a/tests/test_deployment.py b/tests/test_deployment.py index ef24743..1351298 100644 --- a/tests/test_deployment.py +++ b/tests/test_deployment.py @@ -4,11 +4,13 @@ from octue.log_handlers import apply_log_handler from octue.resources import Child, Manifest - apply_log_handler() REPOSITORY_ROOT = os.path.dirname(os.path.dirname(__file__)) +SRUID = "octue/turbsim-service:0.5.1" +BUCKET_NAME = "octue-octue-twined-services-octue-twined" +PROJECT_NAME = "octue-twined-services" class TestDeployment(unittest.TestCase): @@ -16,18 +18,28 @@ class TestDeployment(unittest.TestCase): condition=os.getenv("RUN_DEPLOYMENT_TESTS", "0").lower() == "1", reason="'RUN_DEPLOYMENT_TESTS' environment variable is 0 or not present.", ) - def test_cloud_run_deployment(self): + def test_with_input_file_only(self): """Test that the Google Cloud Run integration works, providing a service that can be asked questions and send responses. An input dataset from Google Cloud Storage is used for this test. """ - input_manifest = Manifest(datasets={"turbsim": "gs://openfast-data/testing/turbsim"}) + child = Child(id=SRUID, backend={"name": "GCPPubSubBackend", "project_name": PROJECT_NAME}) - child = Child( - id="aerosense/turbsim-service", - backend={"name": "GCPPubSubBackend", "project_name": os.environ["TEST_PROJECT_NAME"]}, - ) + input_manifest = Manifest(datasets={"turbsim": f"gs://{BUCKET_NAME}/turbsim-service/testing/turbsim"}) + answer, question_uuid = child.ask(input_manifest=input_manifest, timeout=360) + + self.assertIsNone(answer["output_values"]) + self.assertIsNotNone(answer["output_manifest"]) + self.assertTrue(len(answer["output_manifest"].datasets["turbsim"].files), 1) - answer = child.ask(input_manifest=input_manifest, timeout=360) + def test_with_input_file_and_profile_file(self): + """Test that the deployed service works with an input file and profile file. An input dataset from Google Cloud + Storage is used for this test.""" + child = Child(id=SRUID, backend={"name": "GCPPubSubBackend", "project_name": PROJECT_NAME}) + + input_manifest = Manifest( + datasets={"turbsim": f"gs://{BUCKET_NAME}/turbsim-service/testing/turbsim_with_profile"} + ) + answer, question_uuid = child.ask(input_manifest=input_manifest, timeout=360) self.assertIsNone(answer["output_values"]) self.assertIsNotNone(answer["output_manifest"]) diff --git a/turbsim_service/__init__.py b/turbsim_service/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/turbsim_service/app.py b/turbsim_service/app.py new file mode 100644 index 0000000..07ef823 --- /dev/null +++ b/turbsim_service/app.py @@ -0,0 +1,54 @@ +import datetime +import logging +import os + +from octue.resources import Datafile, Dataset +from octue.utils.files import RegisteredTemporaryDirectory +from octue.utils.processes import run_logged_subprocess + + +logger = logging.getLogger(__name__) + + +OUTPUT_EXTENSION = ".bts" +OUTPUT_FILENAME = "TurbSim" + OUTPUT_EXTENSION + + +def run(analysis): + """Run a turbsim analysis on the input file specified in the input manifest, writing the output file to the cloud. + + :param octue.resources.Analysis analysis: + :return None: + """ + start_datetime = datetime.datetime.now() + + temporary_directory = RegisteredTemporaryDirectory().name + input_dataset = analysis.input_manifest.datasets["turbsim"] + + number_of_files = len(input_dataset.files) + + if number_of_files not in {1, 2}: + raise ValueError( + "The input dataset should only contain either 1 or 2 input files - a 'TurbSim.inp' file and, optionally, " + f"a profile or timeseries file; received {number_of_files} files." + ) + + input_dataset.download(temporary_directory) + + input_file = input_dataset.files.filter(name="TurbSim.inp").one() + logger.info("Starting turbsim analysis.") + run_logged_subprocess(command=["turbsim", input_file.local_path], logger=logger) + + old_output_filename = os.path.splitext(input_file.local_path)[0] + OUTPUT_EXTENSION + + new_temporary_directory = RegisteredTemporaryDirectory().name + new_output_filename = os.path.join(new_temporary_directory, OUTPUT_FILENAME) + os.rename(old_output_filename, new_output_filename) + + # Instantiate a datafile for the output file. + with Datafile(path=new_output_filename, mode="a") as (datafile, f): + datafile.timestamp = start_datetime + datafile.labels = ["turbsim", "output"] + + analysis.output_manifest.datasets["turbsim"] = Dataset(name="turbsim", path=new_temporary_directory) + logger.info("Finished turbsim analysis.") diff --git a/twine.json b/twine.json index 4f8befd..bc04b24 100644 --- a/twine.json +++ b/twine.json @@ -1,12 +1,14 @@ { "input_manifest": { "datasets": { - "turbsim": {"purpose": "A dataset containing a single TurbSim.inp file."} + "turbsim": { + "purpose": "A dataset containing a 'TurbSim.inp' file and, optionally, a profile file or timeseries file." + } } }, "output_manifest": { "datasets": { - "turbsim": {"purpose": "A dataset containing a single TurbSim.bts (binary timeseries) file."} + "turbsim": {"purpose": "A dataset containing a single 'TurbSim.bts' (binary timeseries) file."} } } }