simstack 0.2.0__tar.gz → 2.0.1__tar.gz

{simstack-0.2.0 → simstack-2.0.1}/.dockerignore

@@ -8,6 +8,8 @@ __pycache__
 *.pyo
 *.pyd
 .Python
+.venv
+venv
 pip-log.txt
 pip-delete-this-directory.txt
 .tox
@@ -49,6 +51,7 @@ Thumbs.db
 debug.txt
 *.lock
 !pixi.lock
+!uv.lock
 
 # Build artifacts
 build/

simstack-2.0.1/.github/workflows/ci.yml

@@ -0,0 +1,207 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - "**"
+  pull_request:
+  workflow_dispatch:  # This line enables the manual run button
+
+jobs:
+  smoke:
+    name: Lightweight workflow smoke test
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v8.3.2
+        with:
+          version: "0.11.29"
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+      - name: Set up Python 3.12
+        run: uv python install 3.12
+
+      - name: Install dependencies
+        run: uv sync --all-extras --dev --frozen
+
+      - name: Run lightweight workflow
+        env:
+          START_LOCAL_RUNNER: "false"
+          SIMSTACK_TEST_DB_CONNECTION_STRING: none
+          SIMSTACK_TEST_DB: smoke
+          SIMSTACK_PROJECT_ROOT: ${{ github.workspace }}
+        run: |
+          uv run python -m pytest \
+            tests/with_context/with_runner/test_array_storage_submit.py \
+            tests/with_context/with_runner/test_archive_node_e2e.py \
+            tests/without_context/test_dataset_persisted_structure.py \
+            tests/without_context/test_generate_test.py \
+            -q
+
+  test-linux:
+    name: Test on ubuntu-latest (Python ${{ matrix.python-version }})
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12"]
+
+    services:
+      mongodb:
+        image: mongo:7
+        ports:
+          - 27017:27017
+        env:
+          MONGO_INITDB_ROOT_USERNAME: root
+          MONGO_INITDB_ROOT_PASSWORD: rootpassword
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v8.3.2
+        with:
+          version: "0.11.29"
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+      - name: "Set up Python ${{ matrix.python-version }}"
+        run: uv python install ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: uv sync --all-extras --dev --frozen
+
+      - name: Set up MongoDB for testing
+        run: |
+          uv run python -c "
+          from pymongo import MongoClient
+          client = MongoClient('mongodb://root:rootpassword@localhost:27017/')
+          db = client['admin']
+          db.command('createUser', 'testing', pwd='testpassword', roles=[{'role': 'readWrite', 'db': 'testing_data'}])
+          db = client['testing_data']
+          db['init'].insert_one({'init': True})
+          print('MongoDB initialized with user testing and database testing_data')
+          "
+      - name: Run tests with runner
+        shell: bash
+        env:
+          SIMSTACK_TEST_DB_CONNECTION_STRING: 'mongodb://testing:testpassword@localhost:27017/'
+          SIMSTACK_TEST_DB: testing_data
+          SIMSTACK_PROJECT_ROOT: ${{ github.workspace }}
+        run: |
+          mkdir -p simstack
+          printf '[parameters]\n[parameters.general]\nuse_db = true\nworkdir_self = "${{ github.workspace }}/simstack"\n[parameters.db]\ndatabase = "testing_data"\nconnection_string = "mongodb://testing:testpassword@localhost:27017/"\n' > simstack.toml
+          cat simstack.toml
+          uv run create_model_table --dir tests
+          uv run create_node_table --dir tests
+          START_LOCAL_RUNNER=true uv run python -m pytest \
+            tests/with_context/with_runner/test_runner_completed.py -q
+          START_LOCAL_RUNNER=false uv run python -m pytest tests --junitxml=pytest.xml --cov-report=term-missing --cov=simstack --cov-config=pyproject.toml
+
+  package-html-docs:
+    name: Build Package HTML Docs
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v8.3.2
+        with:
+          version: "0.11.29"
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+      - name: "Set up Python 3.12"
+        run: uv python install 3.12
+
+      - name: Install dependencies
+        run: uv sync --all-extras --dev --frozen
+
+      - name: Generate API documentation sources
+        run: uv run sphinx-apidoc -o doc/source/simstack/modules src/simstack -f
+
+      - name: Build package HTML documentation with Sphinx
+        run: |
+          set -euo pipefail
+          rm -rf src/simstack/static/docs
+          mkdir -p src/simstack/static/docs
+          export SOURCE_DATE_EPOCH="$(git log -1 --format=%ct)"
+          uv run sphinx-build -b html -d /tmp/simstack-docs-doctrees doc/source src/simstack/static/docs
+
+      - name: Upload package HTML documentation artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: sphinx-docs
+          path: src/simstack/static/docs
+
+  test-windows:
+    name: Test on windows-latest (Python ${{ matrix.python-version }})
+    runs-on: windows-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12"]
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Install MongoDB
+        run: |
+          choco install mongodb --no-progress
+          # The service might not start automatically or might need a moment
+          Get-Service MongoDB -ErrorAction SilentlyContinue | Start-Service
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v8.3.2
+        with:
+          version: "0.11.29"
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+      - name: "Set up Python ${{ matrix.python-version }}"
+        run: uv python install ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: uv sync --all-extras --dev --frozen
+
+      - name: Set up MongoDB for testing
+        shell: pwsh
+        run: |
+          uv run python -c "
+          from pymongo import MongoClient
+          client = MongoClient('mongodb://localhost:27017/')
+          db = client['admin']
+          db = client['testing_data']
+          db['init'].insert_one({'init': True})
+          print('MongoDB initialized with database testing_data')
+          "
+
+      - name: Run tests with runner
+        shell: pwsh
+        env:
+          SIMSTACK_TEST_DB_CONNECTION_STRING: 'mongodb://localhost:27017/'
+          SIMSTACK_TEST_DB: testing_data
+          SIMSTACK_PROJECT_ROOT: ${{ github.workspace }}
+        run: |
+          New-Item -ItemType Directory -Force -Path simstack
+          $tomlContent = @"
+          [parameters]
+          [parameters.general]
+          use_db = true
+          workdir_self = "$($env:GITHUB_WORKSPACE -replace '\\', '\\')\\simstack"
+          [parameters.db]
+          database = "testing_data"
+          connection_string = "mongodb://localhost:27017/"
+          "@
+          Set-Content -Path simstack.toml -Value $tomlContent
+          Get-Content simstack.toml
+          uv run create_model_table --dir tests
+          uv run create_node_table --dir tests
+          uv run python -m pytest tests --junitxml=pytest.xml --cov-report=term-missing --cov=simstack --cov-config=pyproject.toml

{simstack-0.2.0 → simstack-2.0.1}/.github/workflows/conda_build.yml

@@ -11,7 +11,7 @@ jobs:
       fail-fast: true
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       - name: Setup Pixi
         uses: prefix-dev/setup-pixi@v0.8.1
         with:

simstack-2.0.1/.github/workflows/notify-simstack-server.yml

@@ -0,0 +1,19 @@
+name: Notify simstack-server to refresh uv.lock
+
+on:
+  push:
+    branches: ["main"]
+
+jobs:
+  dispatch:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Dispatch event to simstack-server
+        env:
+          GH_TOKEN: ${{ secrets.SIMSTACK_SERVER_DISPATCH_TOKEN }}
+        run: |
+          curl -L -X POST \
+            -H "Accept: application/vnd.github+json" \
+            -H "Authorization: Bearer ${GH_TOKEN}" \
+            https://api.github.com/repos/simstack/simstack-server/dispatches \
+            -d '{"event_type":"simstack-main-updated"}'

{simstack-0.2.0 → simstack-2.0.1}/.github/workflows/pypi_build.yml

@@ -10,6 +10,7 @@ defaults:
 jobs:
   build_pypi_package:
     runs-on: ubuntu-latest
+    environment: release
     permissions:
       id-token: write
       contents: read
@@ -19,12 +20,14 @@ jobs:
     if: github.event_name == 'workflow_dispatch' || startsWith(github.ref, 'refs/tags/v')
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0  # Fetch full history to check tag ancestry
 
       - name: Install the latest version of uv
-        uses: astral-sh/setup-uv@v7
+        uses: astral-sh/setup-uv@v8.3.2
+        with:
+          version: "0.11.29"
 
       - name: Verify tag is from main branch
         if: startsWith(github.ref, 'refs/tags/v')

{simstack-0.2.0 → simstack-2.0.1}/.gitignore

@@ -154,3 +154,4 @@ script_runner.out
 *.egg-info
 #version
 src/simstack/_version.py
+.DS_store

{simstack-0.2.0 → simstack-2.0.1}/.pre-commit-config.yaml

@@ -21,16 +21,10 @@ repos:
         exclude: ^(applications|examples|doc|docs)/
   - repo: local
     hooks:
-      - id: pixi-install
-        name: pixi-install
-        entry: pixi install -e mypy
-        language: system
-        always_run: true
-        require_serial: true
-        pass_filenames: false
       - id: mypy
         name: mypy
-        entry: "pixi run -e mypy mypy"
+        entry: uv run mypy --follow-imports=skip
         language: system
-        pass_filenames: false
+        types: [python]
+        exclude: ^(tests|applications|examples|doc|docs)/
         require_serial: true

simstack-2.0.1/MANIFEST.in

@@ -0,0 +1 @@
+recursive-include src/simstack/static/docs *

{simstack-0.2.0/src/simstack.egg-info → simstack-2.0.1}/PKG-INFO

@@ -1,8 +1,8 @@
 Metadata-Version: 2.4
 Name: simstack
-Version: 0.2.0
+Version: 2.0.1
 Summary: A python based workflow engineering platform with a react-js UI
-Author-email: Wolfgang Wenzel <wolfgang.wenzel@kit.edu>, Timo Strunk <timo.strunk@nanomatch.de>
+Author-email: Wolfgang Wenzel <wolfgang.wenzel@kit.edu>, Artem Buildin <artem.buildin@kit.edu>, Nikita Mitagin <nikita.mitagin@kit.edu>, Phillip Dullinger <phillip.dullinger@kit.edu>, Celso Rego <celso.rego@kit.edu>, Oliver Pettkau <oliver.pettkau@kit.edu>, Timo Strunk <timo.strunk@nanomatch.de>
 License: MIT
 Project-URL: Homepage, https://gitlab.kit.edu/kit/ag_wenzel/simstack-model/
 Requires-Python: >=3.12
@@ -13,13 +13,106 @@ Requires-Dist: cloudpickle<4,>=3.1.1
 Requires-Dist: coolname<3,>=2.2.0
 Requires-Dist: nest-asyncio<2,>=1.6.0
 Requires-Dist: numpy>=2.3.0
-Requires-Dist: pandas>=2.3.3
+Requires-Dist: pandas==2.3.2
+Requires-Dist: pytest>=8.4.2
+Requires-Dist: docutils>=0.22
+Requires-Dist: pandas-stubs~=2.3.3
+Requires-Dist: types-docutils~=0.22.3
 Dynamic: license-file
 
-## 1. Install Simstack II — 3-step lightning setup ⚡️
+## SimStack II Overview ⚡️
+
+Simstack II is a workflow orchestration tool that lets you run your workflows on remote 
+resources. 
+
+This repo provides the base package for Simstack II development. To use the graphical user interface,
+you need to install the 
+
+- [simstack-server](https://github.com/simstack/simstack-server) project, a python-based
+fastapi app that connects to the Simstack II database. a
+- [simstack-ui](https://github.com/simstack/simstack-ui) project, a react-js web frontend. 
+
+You can use the [simstack-example](https://github.com/simstack/simstack-example) project 
+to get started. 
+
+## Development workflow and versioning
+
+This repository uses [Gitflow](https://nvie.com/posts/a-successful-git-branching-model/):
+
+- `main` contains production releases.
+- `develop` integrates changes for the next release.
+- `feature-*`|`fix-*` branches start from and merge back into `develop`.
+- `release-*` branches start from `develop`, then merge into both `develop` and `main`.
+- `hotfix-*` branches start from `main`, then merge into both `main` and `develop`.
+-  each `main` merge commit must have a version tag.
+
+Releases follow [Semantic Versioning 2.0.0](https://semver.org/) using
+`MAJOR.MINOR.PATCH`: increment `MAJOR` for incompatible API changes, `MINOR` for
+backward-compatible functionality, and `PATCH` for backward-compatible bug fixes.
+
+### Setting the version
+
+The package version is derived from Git tags by `setuptools-scm`, as configured in
+`pyproject.toml`; it is not maintained in a source file. Do not edit the generated
+`src/simstack/_version.py`.
+
+After the release branch has been merged into `main`, create and push an annotated
+semantic-version tag. Pushing it triggers the PyPI release workflow.
+
+```bash
+git switch main
+git tag -a vX.Y.Z -m "Release vX.Y.Z"
+git push origin vX.Y.Z
+```
+
+
+## Using SimStack II
+
+### Setting Up a MongoDB Instance
+
+SimStack II persists user data via MongoDB, so you need to have a running MongoDB instance.
+
+In a minimal example, you can spin up a MongoDB instance on your local machine with Docker:
+
+```bash
+docker run -d \
+  --name simstack-mongo \
+  -p 27017:27017 \
+  -e MONGO_INITDB_ROOT_USERNAME=admin \
+  -e MONGO_INITDB_ROOT_PASSWORD=yourpassword \
+  mongo:latest
+```
+
+This command:
+
+- Runs MongoDB in detached mode (`-d`)
+- Names the container `simstack-mongo`
+- Maps port 27017 to your localhost
+- Sets up basic authentication with username `admin` and password `yourpassword`
+
+**Important**: Replace `yourpassword` with a secure password and update your `simstack.toml` connection string
+accordingly:
+
+```toml
+connection_string = "mongodb://admin:yourpassword@localhost:27017/"
+```
+You can then create databases and collections in the MongoDB instance with the `mongo` CLI.
+
+### Starting the SimStack II Server
+
+Start the SimStack II server as described in the [simstack-server](https://github.com/simstack/simstack-server) repo.
+Set the `CONNECTION_STRING` environment variable to the connection string for the administration
+database you just created. You can check localhost:8000 to see if the server is running.
+
+### Starting the SimStack II UI
+
+Start the SimStack II UI as described in the [simstack-ui](https://github.com/simstack/simstack-ui) repo.
+You should now be able to access the UI at http://localhost:3000.
+
+
+
+
 
-> **Goal:** create an isolated **`simstack`** environment, pull the model code, and satisfy every dependency in a single
-> coffee break.
 
 | What you’ll do                          | Why it matters                                     |
 |-----------------------------------------|----------------------------------------------------|

simstack-0.2.0/PKG-INFO → simstack-2.0.1/README.md

@@ -1,25 +1,96 @@
-Metadata-Version: 2.4
-Name: simstack
-Version: 0.2.0
-Summary: A python based workflow engineering platform with a react-js UI
-Author-email: Wolfgang Wenzel <wolfgang.wenzel@kit.edu>, Timo Strunk <timo.strunk@nanomatch.de>
-License: MIT
-Project-URL: Homepage, https://gitlab.kit.edu/kit/ag_wenzel/simstack-model/
-Requires-Python: >=3.12
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: odmantic<2,>=1.0.2
-Requires-Dist: cloudpickle<4,>=3.1.1
-Requires-Dist: coolname<3,>=2.2.0
-Requires-Dist: nest-asyncio<2,>=1.6.0
-Requires-Dist: numpy>=2.3.0
-Requires-Dist: pandas>=2.3.3
-Dynamic: license-file
-
-## 1. Install Simstack II — 3-step lightning setup ⚡️
-
-> **Goal:** create an isolated **`simstack`** environment, pull the model code, and satisfy every dependency in a single
-> coffee break.
+## SimStack II Overview ⚡️
+
+Simstack II is a workflow orchestration tool that lets you run your workflows on remote 
+resources. 
+
+This repo provides the base package for Simstack II development. To use the graphical user interface,
+you need to install the 
+
+- [simstack-server](https://github.com/simstack/simstack-server) project, a python-based
+fastapi app that connects to the Simstack II database. a
+- [simstack-ui](https://github.com/simstack/simstack-ui) project, a react-js web frontend. 
+
+You can use the [simstack-example](https://github.com/simstack/simstack-example) project 
+to get started. 
+
+## Development workflow and versioning
+
+This repository uses [Gitflow](https://nvie.com/posts/a-successful-git-branching-model/):
+
+- `main` contains production releases.
+- `develop` integrates changes for the next release.
+- `feature-*`|`fix-*` branches start from and merge back into `develop`.
+- `release-*` branches start from `develop`, then merge into both `develop` and `main`.
+- `hotfix-*` branches start from `main`, then merge into both `main` and `develop`.
+-  each `main` merge commit must have a version tag.
+
+Releases follow [Semantic Versioning 2.0.0](https://semver.org/) using
+`MAJOR.MINOR.PATCH`: increment `MAJOR` for incompatible API changes, `MINOR` for
+backward-compatible functionality, and `PATCH` for backward-compatible bug fixes.
+
+### Setting the version
+
+The package version is derived from Git tags by `setuptools-scm`, as configured in
+`pyproject.toml`; it is not maintained in a source file. Do not edit the generated
+`src/simstack/_version.py`.
+
+After the release branch has been merged into `main`, create and push an annotated
+semantic-version tag. Pushing it triggers the PyPI release workflow.
+
+```bash
+git switch main
+git tag -a vX.Y.Z -m "Release vX.Y.Z"
+git push origin vX.Y.Z
+```
+
+
+## Using SimStack II
+
+### Setting Up a MongoDB Instance
+
+SimStack II persists user data via MongoDB, so you need to have a running MongoDB instance.
+
+In a minimal example, you can spin up a MongoDB instance on your local machine with Docker:
+
+```bash
+docker run -d \
+  --name simstack-mongo \
+  -p 27017:27017 \
+  -e MONGO_INITDB_ROOT_USERNAME=admin \
+  -e MONGO_INITDB_ROOT_PASSWORD=yourpassword \
+  mongo:latest
+```
+
+This command:
+
+- Runs MongoDB in detached mode (`-d`)
+- Names the container `simstack-mongo`
+- Maps port 27017 to your localhost
+- Sets up basic authentication with username `admin` and password `yourpassword`
+
+**Important**: Replace `yourpassword` with a secure password and update your `simstack.toml` connection string
+accordingly:
+
+```toml
+connection_string = "mongodb://admin:yourpassword@localhost:27017/"
+```
+You can then create databases and collections in the MongoDB instance with the `mongo` CLI.
+
+### Starting the SimStack II Server
+
+Start the SimStack II server as described in the [simstack-server](https://github.com/simstack/simstack-server) repo.
+Set the `CONNECTION_STRING` environment variable to the connection string for the administration
+database you just created. You can check localhost:8000 to see if the server is running.
+
+### Starting the SimStack II UI
+
+Start the SimStack II UI as described in the [simstack-ui](https://github.com/simstack/simstack-ui) repo.
+You should now be able to access the UI at http://localhost:3000.
+
+
+
+
+
 
 | What you’ll do                          | Why it matters                                     |
 |-----------------------------------------|----------------------------------------------------|

simstack-2.0.1/doc/source/_static/cobalt2-theme.css

@@ -0,0 +1 @@
+/* Project theme overrides placeholder. */

simstack-2.0.1/doc/source/_static/docs-build-badge.css

@@ -0,0 +1,51 @@
+.bottom-of-page .right-details {
+    display: flex;
+    flex: 1 1 auto;
+    justify-content: flex-end;
+}
+
+.docs-build-badge {
+    display: inline-flex;
+    flex-direction: column;
+    gap: 2px;
+    min-width: 220px;
+    max-width: 340px;
+    margin-left: auto;
+    padding: 9px 12px;
+    border: 1px solid rgba(34, 213, 255, 0.45);
+    border-radius: 12px;
+    background: linear-gradient(145deg, rgba(19, 39, 56, 0.88), rgba(30, 58, 82, 0.88));
+    color: #e9fbff;
+    box-shadow: 0 6px 16px rgba(0, 0, 0, 0.28);
+}
+
+.docs-build-badge__label {
+    font-size: 11px;
+    font-weight: 700;
+    letter-spacing: 0.08em;
+    text-transform: uppercase;
+    color: #7ce9ff;
+}
+
+.docs-build-badge__value {
+    font-size: 13px;
+    font-weight: 600;
+    line-height: 1.3;
+    word-break: break-word;
+}
+
+@media (max-width: 900px) {
+    .bottom-of-page .right-details {
+        justify-content: flex-start;
+    }
+
+    .docs-build-badge {
+        min-width: 180px;
+        max-width: min(72vw, 320px);
+        padding: 8px 10px;
+    }
+
+    .docs-build-badge__value {
+        font-size: 12px;
+    }
+}

simstack-2.0.1/doc/source/_static/docs-build-badge.js

@@ -0,0 +1,51 @@
+(function () {
+    function createBuildBadge() {
+        const script =
+            document.currentScript ||
+            document.querySelector('script[src*="docs-build-badge.js"][data-docs-built-at]');
+
+        if (!script) {
+            return;
+        }
+
+        const builtAt = script.getAttribute("data-docs-built-at");
+        if (!builtAt || document.getElementById("docs-build-badge")) {
+            return;
+        }
+
+        const badge = document.createElement("aside");
+        badge.id = "docs-build-badge";
+        badge.className = "docs-build-badge";
+
+        const label = document.createElement("span");
+        label.className = "docs-build-badge__label";
+        label.textContent = "Docs build";
+
+        const value = document.createElement("span");
+        value.className = "docs-build-badge__value";
+        value.textContent = builtAt;
+
+        badge.appendChild(label);
+        badge.appendChild(value);
+
+        const bottom = document.querySelector(".bottom-of-page");
+        if (!bottom) {
+            return;
+        }
+
+        let rightDetails = bottom.querySelector(".right-details");
+        if (!rightDetails) {
+            rightDetails = document.createElement("div");
+            rightDetails.className = "right-details";
+            bottom.appendChild(rightDetails);
+        }
+
+        rightDetails.appendChild(badge);
+    }
+
+    if (document.readyState === "loading") {
+        document.addEventListener("DOMContentLoaded", createBuildBadge, { once: true });
+    } else {
+        createBuildBadge();
+    }
+})();