mampok 3.0.4__tar.gz

mampok-3.0.4/.gitignore

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+# Python
+__pycache__/
+*.pyc
+*.py[cod]
+*.pyo
+*.pyd
+.Python
+*.egg-info/
+dist/
+build/
+*.egg
+
+# Virtual environments
+.venv/
+venv/
+env/
+
+# Distribution / packaging
+*.whl
+*.tar.gz
+
+# Testing
+.pytest_cache/
+.coverage
+htmlcov/
+.tox/
+
+# IDEs
+.idea/
+.vscode/
+*.swp
+*.swo
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Mampok-specific
+*.log
+mampok_log_*.yml

mampok-3.0.4/.gitlab-ci.yml

@@ -0,0 +1,96 @@
+variables:
+  GIT_SUBMODULE_STRATEGY: normal
+
+stages:          # List of stages for jobs, and their order of execution
+  - pages
+
+# Build documentation
+build-pages:
+  image: python:3.12
+  stage: pages
+  script:
+    - apt-get update -qq && apt-get install -qq -y pandoc  # system install of pandoc is needed
+    - pip install --upgrade pip # carsten 20251208: just to remove warning; no other effect?
+    - pip install "sphinx<9" sphinx-rtd-theme sphinx-toolbox myst_parser nbsphinx nbsphinx_link sphinx-design sphinxcontrib-youtube sphinxcontrib.images
+    - cd docs
+    - make html
+  artifacts:
+    paths:
+      - docs/build/html/
+  rules:
+    - if: $CI_COMMIT_BRANCH == "main" # always for commits to main
+    - if: $CI_COMMIT_BRANCH == "dev"  # always for commits to dev
+    - if: $CI_MERGE_REQUEST_SOURCE_BRANCH_NAME == "dev"
+      when: never   # but not again for any merge requests coming from dev
+    - when: manual  # otherwise manual
+      allow_failure: True  # manual is not required
+
+# Deploy pages for a MR - needs to be separate from deploy-pages-commit due to 
+# $CI_MERGE_REQUEST_SOURCE_BRANCH_NAME != $CI_COMMIT_BRANCH
+deploy-pages-MR:
+  stage: pages
+  needs: 
+    - job: build-pages
+      artifacts: True
+  inherit:
+    default: false
+  environment:
+    name: pages/$CI_MERGE_REQUEST_SOURCE_BRANCH_NAME
+    url: "https://loosolab.pages.gwdg.de/-/software/mampok_v2/-/jobs/$CI_JOB_ID/artifacts/docs/build/html/index.html"
+  artifacts:
+    paths:
+      - docs/build/html/
+  script: 
+    - ls -l docs/
+    - echo "deploy"
+  artifacts:
+    paths:
+      - docs/build/html/
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "merge_request_event" && $CI_MERGE_REQUEST_SOURCE_BRANCH_NAME != "dev" && $CI_MERGE_REQUEST_SOURCE_BRANCH_NAME != "main" # dev/main are built automatically
+      allow_failure: True
+
+# Deploy pages for a commit without a MR
+deploy-pages-commit:
+  stage: pages
+  needs:
+    - job: build-pages
+      artifacts: True
+  inherit:
+    default: false
+  environment:
+    name: pages/$CI_COMMIT_BRANCH
+    url: "https://loosolab.pages.gwdg.de/-/software/mampok_v2/-/jobs/$CI_JOB_ID/artifacts/docs/build/html/index.html"
+  script:
+    - ls -l docs/
+    - echo "deploy" #mv docs/build/html/ public/
+  artifacts:
+    paths:
+      - docs/build/html/
+  rules:
+    - if: $CI_PIPELINE_SOURCE != "merge_request_event"
+      allow_failure: True
+
+# Deploy documentation to public pages if it was the main branch
+pages:
+  stage: pages
+  needs:
+    - job: build-pages
+      artifacts: True
+  inherit:
+    default: false
+  script:
+    - mv docs/build/html/ public/
+  artifacts:
+    paths:
+      - public
+  rules:
+    - if: $CI_COMMIT_BRANCH == "main" # after accepted MR to main
+      allow_failure: False  # main not allowed to fail
+
+
+  
+
+
+
+

mampok-3.0.4/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Loosolab
+
+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:
+
+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.

mampok-3.0.4/PKG-INFO

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+Metadata-Version: 2.4
+Name: mampok
+Version: 3.0.4
+Summary: Kubernetes deployment manager for bioinformatics tools
+Author-email: Jasmin Walter <Jasmin.Walter@mpi-bn.mpg.de>, Noah Knoppik <Noah.Knoppik@mpi-bn.mpg.de>, Philipp Goymann <Philipp.Goymann@mpi-bn.mpg.de>
+License-File: LICENSE
+Requires-Python: >=3.11
+Requires-Dist: boto3
+Requires-Dist: jsonschema
+Requires-Dist: kubernetes<36.0.0
+Requires-Dist: packaging
+Requires-Dist: pyjwt
+Requires-Dist: pyyaml
+Requires-Dist: referencing
+Requires-Dist: typer
+Provides-Extra: dev
+Requires-Dist: pytest; extra == 'dev'
+Requires-Dist: pytest-cov; extra == 'dev'
+Description-Content-Type: text/markdown
+
+<p align="center">
+  <img width=400 src="https://raw.githubusercontent.com/loosolab/MAMPOK/main/docs/source/images/LOGO.png">
+</p>
+
+[![Release](https://img.shields.io/github/v/release/loosolab/MAMPOK)](https://github.com/loosolab/MAMPOK/releases)
+[![PyPI](https://img.shields.io/pypi/v/mampok)](https://pypi.org/project/mampok/)
+[![Documentation](https://img.shields.io/badge/documentation-online-blue)](https://loosolab.pages.gwdg.de/software/mampok_v2/)
+
+**Mampok** (**Ma**naging **M**ultiple **P**rojects **O**n **K**ubernetes) deploys
+containerized bioinformatics tools — Cellxgene, Jupyter, RStudio, IGV, and more — on a
+Kubernetes cluster backed by S3-compatible object storage. You describe your project in a
+JSON file (a *Mamplan*); Mampok handles S3 uploads, Kubernetes resource creation, pod
+readiness checks, and lifecycle management.
+
+For more information about Mampok, please see the [documentation](https://loosolab.pages.gwdg.de/software/mampok_v2/).
+
+## How to install
+
+### Via Python package
+
+Mampok is published in the Python Package Index (PyPI) under the name [mampok](https://pypi.org/project/mampok/).
+It can be installed with the following command:
+
+```bash
+pip install mampok
+```
+
+### Via repository
+
+You can install Mampok directly from the repository with the following commands:
+
+1. Clone the repository:
+
+```bash
+git clone https://github.com/loosolab/MAMPOK
+```
+
+2. Move to the new repository directory:
+
+```bash
+cd MAMPOK
+```
+
+3. Install:
+
+```bash
+pip install .
+```
+
+## Quick start
+
+**1. Create a config file** (pass its path to every command via `--config`):
+
+```json
+{
+  "cluster": {
+    "MY_CLUSTER": {
+      "host": "ingress.example.com",
+      "namespace": "mampok",
+      "kubeconfig_path": "/home/user/.kube/my-cluster-config"
+    }
+  },
+  "s3": {
+    "endpoint": "https://s3.example.com",
+    "access_key": "my-access-key",
+    "secret_key": "my-secret-key",
+    "secretname": "s3-credentials",
+    "prefix": "mampok"
+  },
+  "mamplates_path": "/path/to/mamplates/",
+  "lifetime_days": 30,
+  "mampok_version": ">=2.0.0,<3.0.0"
+}
+```
+
+**2. Create a Mamplan:**
+
+```bash
+mampok create-mamplan \
+  --project-id my-project \
+  --tool cellxgene \
+  --cluster MY_CLUSTER \
+  --owner jdoe \
+  --datatype scRNA-seq \
+  --files data.h5ad \
+  --output ~/mamplans/ \
+  --config /path/to/config.json
+```
+
+**3. Deploy:**
+
+```bash
+mampok deploy ~/mamplans/my-project-mamplan.json --config /path/to/config.json
+```

mampok-3.0.4/README.md

@@ -0,0 +1,94 @@
+<p align="center">
+  <img width=400 src="https://raw.githubusercontent.com/loosolab/MAMPOK/main/docs/source/images/LOGO.png">
+</p>
+
+[![Release](https://img.shields.io/github/v/release/loosolab/MAMPOK)](https://github.com/loosolab/MAMPOK/releases)
+[![PyPI](https://img.shields.io/pypi/v/mampok)](https://pypi.org/project/mampok/)
+[![Documentation](https://img.shields.io/badge/documentation-online-blue)](https://loosolab.pages.gwdg.de/software/mampok_v2/)
+
+**Mampok** (**Ma**naging **M**ultiple **P**rojects **O**n **K**ubernetes) deploys
+containerized bioinformatics tools — Cellxgene, Jupyter, RStudio, IGV, and more — on a
+Kubernetes cluster backed by S3-compatible object storage. You describe your project in a
+JSON file (a *Mamplan*); Mampok handles S3 uploads, Kubernetes resource creation, pod
+readiness checks, and lifecycle management.
+
+For more information about Mampok, please see the [documentation](https://loosolab.pages.gwdg.de/software/mampok_v2/).
+
+## How to install
+
+### Via Python package
+
+Mampok is published in the Python Package Index (PyPI) under the name [mampok](https://pypi.org/project/mampok/).
+It can be installed with the following command:
+
+```bash
+pip install mampok
+```
+
+### Via repository
+
+You can install Mampok directly from the repository with the following commands:
+
+1. Clone the repository:
+
+```bash
+git clone https://github.com/loosolab/MAMPOK
+```
+
+2. Move to the new repository directory:
+
+```bash
+cd MAMPOK
+```
+
+3. Install:
+
+```bash
+pip install .
+```
+
+## Quick start
+
+**1. Create a config file** (pass its path to every command via `--config`):
+
+```json
+{
+  "cluster": {
+    "MY_CLUSTER": {
+      "host": "ingress.example.com",
+      "namespace": "mampok",
+      "kubeconfig_path": "/home/user/.kube/my-cluster-config"
+    }
+  },
+  "s3": {
+    "endpoint": "https://s3.example.com",
+    "access_key": "my-access-key",
+    "secret_key": "my-secret-key",
+    "secretname": "s3-credentials",
+    "prefix": "mampok"
+  },
+  "mamplates_path": "/path/to/mamplates/",
+  "lifetime_days": 30,
+  "mampok_version": ">=2.0.0,<3.0.0"
+}
+```
+
+**2. Create a Mamplan:**
+
+```bash
+mampok create-mamplan \
+  --project-id my-project \
+  --tool cellxgene \
+  --cluster MY_CLUSTER \
+  --owner jdoe \
+  --datatype scRNA-seq \
+  --files data.h5ad \
+  --output ~/mamplans/ \
+  --config /path/to/config.json
+```
+
+**3. Deploy:**
+
+```bash
+mampok deploy ~/mamplans/my-project-mamplan.json --config /path/to/config.json
+```

mampok-3.0.4/docs/Makefile

@@ -0,0 +1,22 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+

mampok-3.0.4/docs/make.bat

@@ -0,0 +1,36 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
+

mampok-3.0.4/docs/source/_static/custom.css

@@ -0,0 +1,142 @@
+.red {
+    color:red;
+}
+
+.blue {
+    color:blue;
+}
+
+/* Table appearance */
+.wy-table-responsive table td, .wy-table-responsive table th {
+    /* !important prevents the common CSS stylesheets from
+       overriding this as on RTD they are loaded after this stylesheet */
+    white-space: normal !important;
+}
+
+/* disabled 20260223 to test fixing missing scroll bar in table; see "FEATURE-COUNT (RNA-Seq only)" table */
+/* .wy-table-responsive {
+    overflow: visible !important;
+} */
+
+
+/* Custom table class with reduced spacings */
+.small-table1 {
+    /* Extend the wy-table-responsive class */
+    @extend .wy-table-responsive;
+    
+    font-size: 16px !important;  /* Table title */
+
+    td, td p {
+        font-size: 8px !important;
+        margin: 0; /* Remove extra spacing */
+        word-break: break-word; /* break long words if needed */
+        overflow-wrap: anywhere; /* handle very long tokens/URLs */
+        padding: 0.1em 0.2em !important; /* Adjust these values as needed */
+    }
+
+    th {
+        font-size: 32px !important;
+        font-weight: normal; /* Optional: Reduce boldness */
+        word-break: break-word; /* break long words if needed */
+        overflow-wrap: anywhere; /* handle very long tokens/URLs */ 
+        padding: 0.1em 0.2em !important; /* Adjust these values as needed */
+    }
+}
+
+/* Custom table class with reduced spacing */
+.small-table2 {
+    /* Extend the wy-table-responsive class */
+    @extend .wy-table-responsive;
+    
+    font-size: 16px !important;  /* Table title */
+
+    td, td p {
+        font-size: 10px !important;
+        margin: 0; /* Remove extra spacing */
+        word-break: break-word; /* break long words if needed */
+        overflow-wrap: anywhere; /* handle very long tokens/URLs */
+        padding: 0.1em 0.2em !important; /* Adjust these values as needed */
+    }
+
+    th {
+        font-size: 32px !important;
+        font-weight: normal; /* Optional: Reduce boldness */
+        word-break: break-word; /* break long words if needed */
+        overflow-wrap: anywhere; /* handle very long tokens/URLs */ 
+        padding: 0.1em 0.2em !important; /* Adjust these values as needed */
+    }
+}
+
+
+/* Custom table class with reduced spacing */
+.small-table3 {
+    /* Extend the wy-table-responsive class */
+    @extend .wy-table-responsive;
+    
+    font-size: 16px !important;  /* Table title */
+
+    td, td p {
+        font-size: 12px !important;
+        margin: 0; /* Remove extra spacing */
+        word-break: break-word; /* break long words if needed */
+        overflow-wrap: anywhere; /* handle very long tokens/URLs */
+        padding: 0.1em 0.2em !important; /* Adjust these values as needed */
+    }
+
+    th {
+        font-size: 32px !important;
+        font-weight: normal; /* Optional: Reduce boldness */
+        word-break: break-word; /* break long words if needed */
+        overflow-wrap: anywhere; /* handle very long tokens/URLs */ 
+        padding: 0.1em 0.2em !important; /* Adjust these values as needed */
+    }
+}
+
+
+/* Custom table class with reduced spacing */
+.small-table4 {
+    /* Extend the wy-table-responsive class */
+    @extend .wy-table-responsive;
+    
+    font-size: 16px !important;  /* Table title */
+
+    td, td p {
+        font-size: 14px !important;
+        margin: 0; /* Remove extra spacing */
+        word-break: break-word; /* break long words if needed */
+        overflow-wrap: anywhere; /* handle very long tokens/URLs */
+        padding: 0.1em 0.2em !important; /* Adjust these values as needed */
+    }
+
+    th {
+        font-size: 32px !important;
+        font-weight: normal; /* Optional: Reduce boldness */
+        word-break: break-word; /* break long words if needed */
+        overflow-wrap: anywhere; /* handle very long tokens/URLs */ 
+        padding: 0.1em 0.2em !important; /* Adjust these values as needed */
+    }
+}
+
+/* Custom table class with reduced spacing */
+.small-table5 {
+    /* Extend the wy-table-responsive class */
+    @extend .wy-table-responsive;
+    
+    font-size: 16px !important;  /* Table title */
+
+    td, td p {
+        font-size: 16px !important;
+        margin: 0; /* Remove extra spacing */
+        word-break: break-word; /* break long words if needed */
+        overflow-wrap: anywhere; /* handle very long tokens/URLs */
+        padding: 0.1em 0.2em !important; /* Adjust these values as needed */
+    }
+
+    th {
+        font-size: 32px !important;
+        font-weight: normal; /* Optional: Reduce boldness */
+        word-break: break-word; /* break long words if needed */
+        overflow-wrap: anywhere; /* handle very long tokens/URLs */ 
+        padding: 0.1em 0.2em !important; /* Adjust these values as needed */
+    }
+}