Merge pull request #575 from tira-io/development

Development
tira-io · Nov 26, 2023 · abd02fc · abd02fc
2 parents 4e94f4f + 48a71a0
commit abd02fc
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diff --git a/.github/workflows/build-documentation-nightly.yml b/.github/workflows/build-documentation-nightly.yml
@@ -13,9 +13,11 @@ jobs:
       - name: Install Dependencies
         run: |
           sudo apt-get install -y python3-pip
-          pip install sphinx furo myst-parser
+          pip install sphinx furo myst-parser sphinx-toolbox
+          pip install pandas pyterrier ir_datasets
           cd python-client/sphinx
-          sphinx-apidoc -o . ../tira
+          # sphinx-apidoc -o . ../tira
+          make doctest
           make html
           touch _build/html/.nojekyll
       - name: Deploy

diff --git a/.github/workflows/build-documentation-production.yml b/.github/workflows/build-documentation-production.yml
@@ -13,9 +13,11 @@ jobs:
       - name: Install Dependencies
         run: |
           sudo apt-get install -y python3-pip
-          pip install sphinx furo myst-parser
+          pip install sphinx furo myst-parser sphinx-toolbox
+          pip install pandas pyterrier ir_datasets
           cd python-client/sphinx
-          sphinx-apidoc -o . ../tira
+          # sphinx-apidoc -o . ../tira
+          make doctest
           make html
           touch _build/html/.nojekyll
       - name: Deploy

diff --git a/.github/workflows/test-python-client-on-many-python-versions.yml b/.github/workflows/test-python-client-on-many-python-versions.yml
@@ -0,0 +1,24 @@
+name: Test Python Client on Many Python Versions
+on: [push]
+
+jobs:
+  image:
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    strategy:
+      matrix:
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+      - name: Build Image
+        run: |
+          cd python-client
+          pip3 install twine coverage-badge python-terrier coverage ir_datasets pytest docker
+          echo running on branch ${GITHUB_REF##*/}
+          pytest
+
diff --git a/application/.devcontainer.json b/application/.devcontainer.json
@@ -1,5 +1,5 @@
 {
-  "image": "webis/tira-application:basis-0.0.93",
+  "image": "webis/tira-application:basis-0.0.94",
   "customizations": {
     "vscode": {
       "extensions": ["ms-python.python", "ms-python.vscode-pylance", "ms-toolsai.jupyter"]

diff --git a/application/Dockerfile.application b/application/Dockerfile.application
@@ -9,7 +9,7 @@ RUN cd /src/tira/frontend-vuetify \
 
 
 # Only change in case of new / updated dependencies
-FROM webis/tira-application:basis-0.0.93
+FROM webis/tira-application:basis-0.0.94
 
 # This Dockerfile ensures that all dependencies do rarely change by starting from a basis image
 # that contains already all dependencies (so that the minor versions do rarely change, but we

diff --git a/application/Dockerfile.application-dev b/application/Dockerfile.application-dev
@@ -1,4 +1,4 @@
-# docker build -t webis/tira-application:basis-0.0.93 -f Dockerfile.application-dev .
+# docker build -t webis/tira-application:basis-0.0.94 -f Dockerfile.application-dev .
 FROM ubuntu:22.04
 
 RUN apt-get update \
@@ -51,3 +51,5 @@ RUN chown -R tira:tira /usr/local && \
 	chown tira:tira -R /home/tira &&\
 	chown tira:tira -R /tira
 
+RUN pip3 install tira==0.0.97 ir-measures==0.3.1
+
diff --git a/application/Makefile b/application/Makefile
@@ -2,8 +2,8 @@
 
 VENV_NAME?=venv
 PYTHON=${PWD}/${VENV_NAME}/bin/python3
-VERSION_APPLICATION=0.0.93
-VERSION_GRPC=0.0.93
+VERSION_APPLICATION=0.0.94
+VERSION_GRPC=0.0.94
 
 .DEFAULT: help
 help:

diff --git a/application/requirements.txt b/application/requirements.txt
@@ -26,3 +26,4 @@ django-extensions
 coverage
 coverage-badge
 discourse-client-in-disraptor==0.0.8
+tira>=0.0.97
diff --git a/application/src/tira/frontend-vuetify/src/submission-components/CodeSubmission.vue b/application/src/tira/frontend-vuetify/src/submission-components/CodeSubmission.vue
@@ -25,24 +25,32 @@
           <v-expansion-panel>
             <v-expansion-panel-title>Step 1: Upload your Code to your repository</v-expansion-panel-title>
             <v-expansion-panel-text>
-              <p>Short conceptual description: deployment + key for git repo, deployment + key of tira key</p>
+              <p>Your  <a :href="http_repo_url" target="_blank">prepared Github repository</a> already contains all secrets to build and upload your code as Docker image to TIRA and makes it easier for us to help you in case of problems because we can access the code.</p>
+
               <p>If you start from scratch, you can just <a :href="http_repo_url" target="_blank">clone your repository</a>.</p>
 
-              <code-snippet title="Merge your existing repository" :code="code_for_merging" expand_message="If you already have a git repository, please merge it with the tira repository."/>
+              <code-snippet title="Merge your existing repository (intended as second upstream)" :code="code_for_merging" expand_message="If you already have a git repository, please merge it with the tira repository that is intended as second remote/upstream."/>
             </v-expansion-panel-text>
           </v-expansion-panel>
 
           <v-expansion-panel>
             <v-expansion-panel-title>Step 2: Build your Docker image via GitHub Actions</v-expansion-panel-title>
             <v-expansion-panel-text>
-              <p>step by step description</p>
+              <p>Please go to your <a :href="http_repo_url" target="_blank">prepared Github repository</a> and upload your code to the repository. Upon initialization, your repository contains a jupyter notebook
+              <a :href="http_repo_url + '/blob/main/jupyter-notebook-submissions/pyterrier-notebook.ipynb'" target="_blank">Jupyter notebook</a> together with <a :href="http_repo_url +'/tree/main/jupyter-notebook-submissions'" target="_blank">a detailed README on how to submit together with background information</a>.</p>
+
+              <p>In short, navigate to "Actions" -> "upload-notebook-submission" in <a :href="http_repo_url" target="_blank">your Github repository</a> and click on "Run workflow" to start the Github action that builds, tests, and uploads your submission.</p>
+
+              <p>You can also watch the <a href="https://conf.fmi.uni-leipzig.de/playback/presentation/2.3/9d654239893aee5d164d92e3b2263ab510249eea-1700482128152" target="_blank">recording of the tutorial</a> from the IR lab in Leipzig from teh 20.11.2023.</p>
             </v-expansion-panel-text>
           </v-expansion-panel>
 
           <v-expansion-panel>
             <v-expansion-panel-title>Step 3:Execute your Docker image in TIRA</v-expansion-panel-title>
             <v-expansion-panel-text>
-              <p>step by step description</p>
+              <p>After your Github action was successfull, it prints out the name under which your software was added to TIRA as Docker submission (at the very bottom of the step "Build, test, and upload image" of your Github action). Click on the Docker tab and select your newly added software (maybe reload the page). Select the dataset on which you want to execute your software together with the execution instance (e.g., 1CPU + 10GB of RAM) and click on RUN to start your submission. Admins will review your submission (might take up to one day) and reach out to you in case there are problems with the execution.</p>
+
+              <p>You can also watch the <a href="https://conf.fmi.uni-leipzig.de/playback/presentation/2.3/9d654239893aee5d164d92e3b2263ab510249eea-1700482128152" target="_blank">recording of the tutorial</a> from the IR lab in Leipzig from teh 20.11.2023.</p>
             </v-expansion-panel-text>
           </v-expansion-panel>
         </v-expansion-panels>

diff --git a/application/src/tira/git_runner_integration.py b/application/src/tira/git_runner_integration.py
@@ -27,8 +27,9 @@
 logger = logging.getLogger('tira')
 
 
-def normalize_file(file_content, tira_user_name):
-    return file_content.replace('TIRA_USER_FOR_AUTOMATIC_REPLACEMENT', tira_user_name)
+def normalize_file(file_content, tira_user_name, task_id):
+    return file_content.replace('TIRA_USER_FOR_AUTOMATIC_REPLACEMENT', tira_user_name)\
+        .replace('TIRA_TASK_ID_FOR_AUTOMATIC_REPLACEMENT', task_id)
 
 
 def convert_size(size_bytes):
@@ -1216,9 +1217,7 @@ def create_software_submission_repository_for_user(self, reference_repository_na
         repo.create_secret('TIRA_DOCKER_REGISTRY_USER', dockerhub_user)
         repo.create_secret('TIRA_CLIENT_TOKEN', tira_client_token)
         repo.create_secret('TIRA_CLIENT_USER', tira_client_user)
-        repo.create_secret('TIRA_TASK_ID', tira_task_id)
         repo.create_secret('TIRA_CODE_REPOSITORY_ID', tira_code_repository_id)
-        repo.create_secret('TIRA_VM_ID', tira_user_name)
 
         contents = reference_repo.get_contents(repository_search_prefix)
         while contents:
@@ -1227,7 +1226,7 @@ def create_software_submission_repository_for_user(self, reference_repository_na
                 contents.extend(reference_repo.get_contents(file_content.path))
             else:
                 decoded_content = file_content.decoded_content.decode()
-                decoded_content = normalize_file(decoded_content, tira_user_name)
+                decoded_content = normalize_file(decoded_content, tira_user_name, tira_task_id)
                 repo.create_file(file_content.path, 'Initial Commit.', decoded_content)
 
         return repo

diff --git a/python-client/Dockerfile.dev b/python-client/Dockerfile.dev
@@ -33,7 +33,7 @@ USER dev
 
 RUN pip3 install twine coverage-badge python-terrier coverage
 RUN pip3 install pytest docker
-RUN pip3 install sphinx furo myst-parser
+RUN pip3 install sphinx furo myst-parser sphinx-toolbox
 RUN pip3 install tira \
 	&& cd /tmp \
 	&& python3 -c 'from tira.third_party_integrations import ensure_pyterrier_is_loaded; ensure_pyterrier_is_loaded();' \

diff --git a/python-client/Makefile b/python-client/Makefile
@@ -3,7 +3,7 @@
 build-pypi-package: run-tests
 	python3 -m build --sdist .
 	python3 -m build --wheel .
-	twine upload dist/tira-0.0.93-py3-none-any.whl dist/tira-0.0.93.tar.gz
+	twine upload dist/tira-0.0.97-py3-none-any.whl dist/tira-0.0.97.tar.gz
 
 run-tests:
 	docker run -u root --rm -v /var/run/docker.sock:/var/run/docker.sock -v ${PWD}:/app -w /app --entrypoint pytest webis/tira:python-client-dev-0.0.4

diff --git a/python-client/pyproject.toml b/python-client/pyproject.toml
@@ -0,0 +1,2 @@
+[tool.black]
+line-length = 120
diff --git a/python-client/setup.cfg b/python-client/setup.cfg
@@ -41,3 +41,10 @@ console_scripts =
     tira-run = tira.tira_run:main
     tira-run-notebook = tira.tira_run_notebook:main
     tira-run-inference-server = tira.tira_run_inference_server:main
+
+[flake8]
+max-line-length = 120
+extend-ignore = E203
+
+[isort]
+profile=black
diff --git a/python-client/sphinx/_static/css/custom.css b/python-client/sphinx/_static/css/custom.css
@@ -0,0 +1,16 @@
+details {
+    border: 2pt solid var(--color-background-border);
+    background-color: var(--color-background-secondary);
+    margin: 2pt;
+    padding: 0pt 10pt;
+}
+
+details > summary {
+    padding: 2pt 0pt;
+    cursor: pointer;
+    font-weight: bold;
+}
+
+details[open] > summary {
+    border-bottom: 2pt solid var(--color-background-border);
+}
diff --git a/python-client/sphinx/api.rst b/python-client/sphinx/api.rst
diff --git a/python-client/sphinx/changelog.rst b/python-client/sphinx/changelog.rst
diff --git a/python-client/sphinx/conf.py b/python-client/sphinx/conf.py
@@ -12,7 +12,7 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../tira/'))
+sys.path.insert(0, os.path.abspath('../'))
 
 
 # -- Project information -----------------------------------------------------
@@ -29,9 +29,22 @@
 # ones.
 extensions = [
     'sphinx.ext.autodoc',
+    'sphinx.ext.todo',
+    'sphinx.ext.doctest',
+    'sphinx.ext.viewcode',
+    'sphinx_toolbox.collapse',
     'myst_parser',
 ]
 
+todo_include_todos=True
+python_display_short_literal_types=True
+python_use_unqualified_type_names=True
+viewcode_line_numbers=True
+
+doctest_global_setup = '''
+from tira.io_utils import *
+'''
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
@@ -50,6 +63,7 @@
 html_title = 'TIRA'
 language = 'en'
 
+html_logo = "https://github.com/tira-io/tira-branding/raw/master/tira-icons/logo-tira-120x120-transparent.png"
 html_theme_options: Dict[str, Any] = {
     "footer_icons": [
         {
@@ -66,10 +80,16 @@
     "source_repository": "https://github.com/tira-io/tira",
     "source_branch": "development",
     "source_directory": "python-client/sphinx",
+    "sidebar_hide_name": True,
+    "navigation_with_keys": True,
 }
 
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ['_static']
+
+html_css_files = [
+    'css/custom.css',
+]
diff --git a/python-client/sphinx/contributing/index.rst b/python-client/sphinx/contributing/index.rst
diff --git a/python-client/sphinx/contributing/internals.rst b/python-client/sphinx/contributing/internals.rst
diff --git a/python-client/sphinx/development/backend/index.rst b/python-client/sphinx/development/backend/index.rst
@@ -0,0 +1,8 @@
+Backend Development
+===================
+.. todo:: add a nice introductory text and thank for the interest in helping out for further TIRA
+
+.. toctree::
+    :hidden:
+
+    workflow
diff --git a/python-client/sphinx/development/backend/workflow.rst b/python-client/sphinx/development/backend/workflow.rst
@@ -0,0 +1,32 @@
+Workflow
+========
+.. todo:: add nice introductory text
+
+Getting Started
+---------------
+Initial Setup
+~~~~~~~~~~~~~
+.. todo:: how do I start working on TIRA?
+
+Running TIRA locally
+~~~~~~~~~~~~~~~~~~~~
+.. todo:: How to run tira locally
+
+
+Commands
+--------
+Linting
+~~~~~~~
+.. todo:: What commands are used for linting
+
+Unit Tests
+~~~~~~~~~~
+.. todo:: How to start the unit tests
+
+Generating documentation
+~~~~~~~~~~~~~~~~~~~~~~~~
+.. todo:: How to generate documentation
+
+Releasing a new version
+~~~~~~~~~~~~~~~~~~~~~~~
+.. todo:: How to release a new version
diff --git a/python-client/sphinx/development/changelog.rst b/python-client/sphinx/development/changelog.rst
@@ -0,0 +1,3 @@
+Changelog
+=========
+.. todo:: This page will log changes once we reached the 1.0.0 release
diff --git a/...client/sphinx/contributing/guidelines.rst → ...x/development/contributing/guidelines.rst b/...client/sphinx/contributing/guidelines.rst → ...x/development/contributing/guidelines.rst
@@ -1,4 +1,4 @@
 Contribution Guidelines
 =======================
 
-.. include:: ../../../CONTRIBUTING.md
+.. include:: ../../../../CONTRIBUTING.md
diff --git a/python-client/sphinx/development/contributing/index.rst b/python-client/sphinx/development/contributing/index.rst
@@ -0,0 +1,9 @@
+Contributing
+============
+.. todo:: add a nice introductory text and thank for the interest in helping out for further TIRA
+
+.. toctree::
+    :hidden:
+
+    internals
+    guidelines
diff --git a/python-client/sphinx/development/contributing/internals.rst b/python-client/sphinx/development/contributing/internals.rst
@@ -0,0 +1,12 @@
+Internals
+=========
+
+.. todo:: add nice introductory text
+
+Repository Layout
+-----------------
+.. todo:: What does the Repository structure look like
+
+Architecture
+------------
+.. todo:: document what components make up TIRA, what purpose they serve and how they work with each other
diff --git a/python-client/sphinx/development/frontend/index.rst b/python-client/sphinx/development/frontend/index.rst
@@ -0,0 +1,8 @@
+Frontend Development
+====================
+.. todo:: add a nice introductory text and thank for the interest in helping out for further TIRA
+
+.. toctree::
+    :hidden:
+
+    workflow