ctao-calibpipe 0.1.0__tar.gz

ctao_calibpipe-0.1.0/.dockerignore

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+**/__pycache__
+**/*.pyc
+**/*.egg-info
+**/build

ctao_calibpipe-0.1.0/.gitattributes

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+*.simtel.gz filter=lfs diff=lfs merge=lfs -text

ctao_calibpipe-0.1.0/.gitignore

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+.pytest_cache
+*.log
+
+# Compiled files
+*.py[co]
+*.a
+*.o
+*.so
+__pycache__
+*.svg
+*.png
+
+# ignore version cache file (generated automatically when setup.py is run)
+src/calibpipe/_version.py
+
+# Ignore .c files by default to avoid including generated code. If you want to
+# add a non-generated .c extension, use `git add -f filename.c`.
+*.c
+
+# Other generated files
+*/cython_version.py
+htmlcov
+.coverage*
+MANIFEST
+
+# Sphinx
+docs/source/calibpipe_api
+docs/_build
+
+# Editors and IDEs
+
+# Visual Studio Code
+.vscode
+# Eclipse
+.project
+.pydevproject
+.settings
+# Pycharm
+.idea
+# KDevelop
+*kdev4
+
+# Packages/installer info
+*.egg
+*.eggs
+*.egg-info
+dist
+build
+eggs
+parts
+bin
+var
+sdist
+develop-eggs
+.installed.cfg
+distribute-*.tar.gz
+
+# Other
+.*.swp
+*~
+\#*
+.\#*
+
+# Mac OSX
+.DS_Store
+
+# Rope refactoring data:
+.ropeproject
+
+# ipython notebook checkpoints
+.ipynb_checkpoints
+.cache*
+.cache
+
+*.out
+
+#sonarlint command-line output
+.sonarlint
+
+# output files (should not be stored in git)
+*.h5
+*.hdf5
+*.fits
+*.fits.gz
+*.grib2
+
+*.pstats
+target
+.mypy_cache
+
+examples/notebooks/*.html
+examples/notebooks/*.png

ctao_calibpipe-0.1.0/.gitlab/issue_templates/Bug.md

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+### Summary
+<!--- Summarize the bug encountered concisely -->
+
+
+### Steps to reproduce
+<!--- How one can reproduce the issue - this is very important -->
+
+
+### What is the expected correct behavior?
+<!--- What you should see instead -->
+
+
+### Relevant logs and/or screenshots
+<!--- Paste any relevant logs - please use code blocks (```) to format -->
+<!--- console output, logs, and code as it's very hard to read otherwise -->
+
+
+### Environment
+
+- Version used:
+- Operation System:
+
+
+<!--- ### Possible fixes -->
+<!--- If you can, link to the line of code that might be responsible for the problem -->
+
+
+/label ~bug

ctao_calibpipe-0.1.0/.gitlab/issue_templates/Discussion.md

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+### Summary
+<!--- Summarize what you would like to discuss -->
+<!--- and what is the actual behavior -->
+
+
+### What is the expected correct behavior?
+<!--- What you should see instead -->
+
+
+### Relevant logs and/or screenshots
+<!--- Paste any relevant logs - please use code blocks (```) to format -->
+<!--- console output, logs, and code as it's very hard to read otherwise -->
+
+
+/label ~discussion

ctao_calibpipe-0.1.0/.gitlab/issue_templates/default.md

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+### Summary
+<!--- Summarize the new feature you would like to add concisely -->
+<!--- and describe the actual behavior -->
+
+
+### What is the expected correct behavior?
+<!--- What you should see instead -->
+
+
+### Relevant logs and/or screenshots
+<!--- Paste any relevant logs - please use code blocks (```) to format -->
+<!--- console output, logs, and code as it's very hard to read otherwise -->
+
+
+<!--- ### Possible fixes -->
+<!--- If you can, provide a code snippet which may implement the requested feature -->
+
+
+/label ~enhancement

ctao_calibpipe-0.1.0/.gitlab/merge_request_templates/default.md

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+## Description
+<!--- Describe your changes in detail -->
+
+### Commits
+%{all_commits}
+
+## Related Issue
+<!--- This project only accepts pull requests related to open issues -->
+<!--- If suggesting a new feature or change, please discuss it in an issue first -->
+<!--- If fixing a bug, there should be an issue describing it with steps to reproduce -->
+<!--- If addressing multiple issues, comment on their relation if needed -->
+<!--- Please link issues accordgin to the automation rules: -->
+<!--- https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically -->
+
+## How Has This Been Tested?
+<!--- Please describe in detail how you tested your changes. -->
+<!--- Include details of your testing environment, and the tests you ran to -->
+<!--- see how your change affects other areas of the code, etc. -->
+
+<!--- ## Screenshots (if appropriate): -->
+
+## Types of changes
+<!--- What types of changes does your code introduce? Put an `x` in all the boxes that apply: -->
+- [ ] Bug fix (non-breaking change which fixes an issue)
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to change)
+
+## Checklist:
+<!--- Go over all the following points, and put an `x` in all the boxes that apply. -->
+<!--- If you're unsure about any of these, don't hesitate to ask. We're here to help! -->
+- [ ] My code follows the code style of this project.
+- [ ] My change requires a change to the documentation.
+- [ ] I have updated the documentation accordingly.
+- [ ] I have read the **CONTRIBUTING** document.
+- [ ] I have added tests to cover my changes.
+- [ ] All new and existing tests passed.

ctao_calibpipe-0.1.0/.gitlab-ci.yml

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+#
+include:
+  - project: 'cta-computing/dpps/aiv/dpps-aiv-toolkit'
+    ref: dd87c1aaf379ece916a8e11c069e79d07b521b56
+    file: 'ci-functions.yml'
+
+  - 'aiv-config.yml'
+
+variables:
+  CHART_LOCATION: chart
+  CHART_NAME: calibpipe
+  CHART_EXTRA_VALUES: "--set dev.client_image_tag=${DOCKER_TAG}"
+  DPPS_AIV_TOOLKIT_DIR: dpps-aiv-toolkit
+  CONDA_IMAGE: "quay.io/condaforge/miniforge3:24.11.3-0"
+
+stages:
+    - prepare
+    - lint
+    - build
+    - tests
+    - sonarqube
+    - report
+    - doc
+    - publish
+
+default:
+    image: harbor.cta-observatory.org/proxy_cache/python:3.12
+
+variables:
+    CTAPIPE_VERSION: 'latest'
+#
+# Anchors definition
+#
+.env_template: &env_setup
+    before_script:
+        - apt-get install git
+        - pip install pylint pylint-exit anybadge
+        - |-
+            if [ "$CTAPIPE_VERSION" = "nightly" ]; then
+              pip install git+https://github.com/cta-observatory/ctapipe.git
+            fi
+        - echo -n $RDAMS_TOKEN > rdams_token.txt
+        - >
+          echo "url: https://cds.climate.copernicus.eu/api" > ~/.cdsapirc
+        - >
+          echo "key: $CDS_KEY" >> ~/.cdsapirc
+        - cp ~/.cdsapirc ./
+
+.unittest_template:
+    stage: tests
+    needs: []
+    <<: *env_setup
+    script:
+        - pip install .[test]
+        - pytest -v --cov=calibpipe --junitxml=report.xml -m "not gdas and not db and not integration"
+    artifacts:
+        when: always
+        reports:
+            junit: report.xml
+
+#
+# Jobs
+#
+pylint:
+    stage: lint
+    needs: []
+    <<: *env_setup
+    script:
+        - pip install .[test]
+        - mkdir ./pylint
+        - pylint --fail-under 5.0 ./src/calibpipe/ --output-format=json2:pylint.json,colorized | tee ./pylint/pylint.log || pylint-exit $?
+        - PYLINT_SCORE=$(sed -n 's/^Your code has been rated at \([-0-9.]*\)\/.*/\1/p' ./pylint/pylint.log)
+        - anybadge --label=Pylint --file=pylint/pylint.svg --value=$PYLINT_SCORE 2=red 4=orange 8=yellow 10=green
+        - echo "Pylint score is $PYLINT_SCORE"
+    artifacts:
+        paths:
+            - ./pylint/
+            - pylint.json
+
+unittests:
+    parallel:
+        matrix:
+        - PYTHON_VERSION: ["3.10", "3.11", "3.12", latest]
+          CTAPIPE_VERSION: [nightly, latest]
+    image: harbor.cta-observatory.org/proxy_cache/python:$PYTHON_VERSION
+    rules:
+        - if: '$PYTHON_VERSION == "latest" && $CTAPIPE_VERSION == "latest"'
+          allow_failure: true
+        - if: '$CTAPIPE_VERSION == "nightly"'
+          allow_failure: true
+        - if: '$CTAPIPE_VERSION'
+          allow_failure: false
+        - if: '$PYTHON_VERSION == "latest"'
+          allow_failure: true
+        - if: '$PYTHON_VERSION'
+          allow_failure: false
+    extends: [.unittest_template]
+
+test:
+    stage: tests
+    <<: *env_setup
+    services:
+        - name: harbor.cta-observatory.org/proxy_cache/postgres:17
+          alias: postgres
+    variables:
+        POSTGRES_DB: TEST_CALIBPIPE_DB
+        POSTGRES_USER: TEST_CALIBPIPE_DB_USER
+        POSTGRES_PASSWORD: DUMMY_PSWRD
+        POSTGRES_HOST_AUTH_METHOD: trust
+    script:
+        - pip install -e .[test]
+        - pip install coverage-badge
+        - mkdir -pv test
+        - pytest -v --cov=calibpipe --junitxml=test/report.xml  --cov-report=xml:test/coverage.xml
+        - coverage-badge
+    coverage: '/TOTAL.+ ([0-9]{1,3}%)/'
+    artifacts:
+        when: always
+        reports:
+            junit: test/report.xml
+        paths:
+            - test/coverage.xml
+            - test/report.xml
+            - "*.ecsv"
+            - "*.log"
+
+build-docs:
+    before_script:
+        - apt-get install -y curl
+        - curl -fsSL https://deb.nodesource.com/setup_current.x | bash -
+        - apt-get install -y nodejs
+        - apt-get install -y --no-install-recommends chromium libnss3
+        - npm install -g playwright
+        - npm install -g @mermaid-js/mermaid-cli
+        - export PUPPETEER_SKIP_CHROMIUM_DOWNLOAD=true
+        - export PUPPETEER_EXECUTABLE_PATH=$(which chromium-browser)
+        - python --version
+        - pip install .[doc]
+
+publish-chart:
+  rules:
+    - when: never
+
+collect-test-artifacts:
+    needs:
+    - job: unittests
+      artifacts: true
+    - job: test
+      artifacts: true
+    - job: collect-manual-tests
+      artifacts: true
+
+k8s-integration-tests:
+    rules:
+    - when: never

ctao_calibpipe-0.1.0/.gitmodules

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+[submodule "dpps-aiv-toolkit"]
+	path = dpps-aiv-toolkit
+	url = ../../aiv/dpps-aiv-toolkit.git

ctao_calibpipe-0.1.0/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0  # Use the ref you want to point at
+    hooks:
+    - id: trailing-whitespace
+      exclude: ".*\\.fits(\\.fz)?"
+    - id: check-added-large-files
+    - id: check-case-conflict
+    - id: check-merge-conflict
+      exclude: ".*\\.fits(\\.fz)?"
+    - id: end-of-file-fixer
+      exclude: '(.*\.fits(\.fz)?)|(.*.patch.*)|(chart\/.*README.md)$'
+
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
+    hooks:
+    - id: codespell
+      additional_dependencies:
+        - tomli
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.2.1
+    hooks:
+      - id: ruff
+        args: [ --fix, --show-fixes ]
+      - id: ruff-format
+
+  - repo: local
+    hooks:
+    - id: CI yaml check
+      args: [ dpps-aiv-toolkit ]
+      name: CI yaml check
+      description: CI yaml check
+      language: script
+      entry: dpps-aiv-toolkit/cicheck.sh
+      pass_filenames: false
+      always_run: true
+
+
+  - repo: https://github.com/norwoodj/helm-docs
+    rev: "v1.14.2"
+    hooks:
+    - id: helm-docs-built
+      args:
+        - "--chart-search-root=chart"

ctao_calibpipe-0.1.0/AUTHORS.md

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+# CONTRIBUTORS
+
+## Current team members
+- Leonid Burmistrov
+- Mykhailo Dalchenko
+- Tjark Miener
+- Georgios Voutsinas
+
+## Former team members
+- Gabriel Emery
+- Antonio Di Pilato
+- Gregoire Uhlrich
+- Vadym Voitsekhovskyi

ctao_calibpipe-0.1.0/CONTRIBUTING.md

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+# Contributing to DPPS CalibPipe
+
+As main contributors are affiliated with the University of Geneva, we respect its [Code of Conduct][coc] and ask you to do the same.
+
+## Questions, Bugs, Features
+
+### Found an Issue or Bug?
+
+If you find a bug in the source code, you can help us by submitting a Bug Report to our [GitLab Repository][gitlab-issues]. Even better, you can submit a Merge Request with a fix.
+
+### Missing a Feature?
+
+You can request a new feature by submitting an issue to our [GitLab Repository][gitlab-issues]. If you would like to implement a new feature, it should be discussed first in a [GitLab issue][gitlab-issues] that clearly outlines the changes and benefits of the feature.
+
+### Want a Doc Fix?
+
+If you have a suggestion for the documentation, you can open an issue and outline the problem or improvement you have. Creating the doc fix yourself is even better! For large fixes, please build and test the documentation before submitting the PR to ensure you haven't introduced any layout or formatting issues. Make sure your commit message follows the [Commit Message Guidelines][developers-commits].
+
+## Issue Submission Guidelines
+
+Before you submit your issue, search the archive to see if your question was already answered. If your issue appears to be a bug and hasn't been reported, open a new issue. Help us maximize the effort we can spend fixing issues and adding new features by not reporting duplicate issues.
+
+The "[new issue][gitlab-new-issue]" form contains a number of predefined templates under the **Description** drop-down. Please select the relevant issue template and fill it out to simplify the understanding and proper treatment of the issue. Please add one of the following labels to your issue: `bug`, `suggestion`, `enhancement`, `discussion`, `documentation`, `question`. Do not add other labels or assign developers; this will be done by the project management.
+
+## Merge Request Submission Guidelines
+
+Before you submit your merge request, consider the following guidelines:
+
+1. Search [GitLab][gitlab-merge-requests] for an open or closed Merge Request that relates to your submission to avoid duplicating effort.
+<!-- 2. Create the [development environment](../getting_started/index.rst#development_setup). -->
+2. Create the development environment following the instructions in {ref}`development_setup`.
+3. Make your changes in a new git branch:
+    ```shell
+    git checkout -b my-fix-branch main
+    ```
+    - You do not need to fork the repository; instead, create a new branch in the central repository.
+    - The branch name should follow the regular expression `(feature|bugfix|cleanup)/*` and be meaningful.
+4. Create your patch commit, including appropriate test cases.
+    - If it's your first commit in this repository, add yourself to the `AUTHORS` file.
+5. Follow our Code Style Guidelines (they are enforced by the precommit hooks, don't forget to install them!):
+    - [PEP8][pep8] standard for python code.
+    - [numpydoc][numpydoc] for the documentation.
+6. If the changes affect public APIs, change or add relevant documentation.
+7. Commit your changes using a descriptive commit message that follows our [commit message conventions][developers-commits].
+    ```shell
+    git add <list of files you have modified>
+    git commit
+    ```
+    Note: Do not add binary files, libraries, build artifacts, etc., to your commit.
+8. Push your branch to GitLab:
+    ```shell
+    git push origin my-fix-branch
+    ```
+9. Test your code following the testing instructions.
+10. In GitLab, open a merge request to `calibPipe:main` and fill out the merge request template.
+11. If we suggest changes:
+    - Make the required updates.
+    - Re-run all applicable tests.
+    - Commit your changes to your branch (e.g., `my-fix-branch`).
+    - Push the updated branch to the GitLab repository (this will update your Merge Request).
+    - You can also amend the initial commits and force push them to the branch:
+        ```shell
+        git rebase main -i
+        git push origin my-fix-branch -f
+        ```
+
+## After Your Merge Request is Merged
+
+After your merge request is merged, the branch you created will be automatically deleted from the central repository.
+
+1. Check out the main branch:
+    ```shell
+    git checkout main -f
+    ```
+2. Delete the local branch:
+    ```shell
+    git branch -D my-fix-branch
+    ```
+3. Update your main with the latest upstream version:
+    ```shell
+    git pull --ff origin main
+    ```
+
+[coc]: https://www.unige.ch/ethique/charter/
+[gitlab]: https://gitlab.cta-observatory.org/cta-computing/dpps/calibrationpipeline/calibpipe
+[gitlab-issues]: https://gitlab.cta-observatory.org/cta-computing/dpps/calibrationpipeline/calibpipe/-/issues
+[gitlab-merge-requests]: https://gitlab.cta-observatory.org/cta-computing/dpps/calibrationpipeline/calibpipe/-/merge_requests
+[developers-commits]: https://chris.beams.io/posts/git-commit/
+[gitlab-new-issue]: https://gitlab.cta-observatory.org/cta-computing/dpps/calibrationpipeline/calibpipe/-/issues/new
+[pep8]: https://www.python.org/dev/peps/pep-0008/
+[numpydoc]: https://numpydoc.readthedocs.io/en/latest/

ctao_calibpipe-0.1.0/Dockerfile

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+# See https://testdriven.io/blog/docker-best-practices/ for recommendations
+# on writing dockerfiles for python projects.
+
+# We use a build stage to build a wheel which we then copy and install
+# in the second stage to minimize image size. This is mostly needed
+# because setuptools_scm needs the full version info from git and git
+# itself but including that in the final image would bloat its size.
+
+# we are using the official python image with just a version tag here
+# it comes with many tools needed to build and compile python packages
+# which increases it's size but is helpful for building
+FROM harbor.cta-observatory.org/proxy_cache/python:3.12 AS builder
+
+
+# Copy full repo, needed for setuptools_scm to properly report version
+COPY . /repo/
+
+# build the wheel
+RUN python -m pip install --no-cache-dir build && cd repo && python -m build --wheel
+
+
+# second stage, copy and install wheel
+# We are using the official python 3.11 image
+# as base image in the slim variant to reduce image size.
+FROM harbor.cta-observatory.org/proxy_cache/python:3.12-slim
+COPY --from=builder /repo/dist /tmp/dist
+
+RUN apt-get update && \
+    apt-get -y install gcc mono-mcs && \
+    apt-get -y install libeccodes-dev && \
+    rm -rf /var/lib/apt/lists/*
+
+RUN python -m pip install --no-cache-dir /tmp/dist/* \
+    && rm -r /tmp/dist
+
+RUN addgroup --system ctao && adduser --system --group ctao
+USER ctao

ctao_calibpipe-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright 2022 CTA DPPS Calibration Pipeline Authors
+
+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.

ctao_calibpipe-0.1.0/PKG-INFO

@@ -0,0 +1,86 @@
+Metadata-Version: 2.4
+Name: ctao-calibpipe
+Version: 0.1.0
+Author: Leonid Burmistrov, Mykhailo Dalchenko, Antonio Di Pilato, Gabriel Emery, Tjark Miener, Gregoire Uhlrich, Georgios Voutsinas, Vadym Voitsekhovskyi
+Classifier: License :: OSI Approved :: MIT License
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: AUTHORS.md
+Requires-Dist: astral
+Requires-Dist: astropy
+Requires-Dist: cdsapi
+Requires-Dist: ctapipe>=0.18
+Requires-Dist: h5py
+Requires-Dist: molecularprofiles>=2.1.0
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: psycopg[binary]
+Requires-Dist: pygrib
+Requires-Dist: pyrdams>=3.0.1
+Requires-Dist: requests>=2.27
+Requires-Dist: requests
+Requires-Dist: sqlalchemy>=2.0.1
+Requires-Dist: traitlets
+Provides-Extra: test
+Requires-Dist: black>=22.5; extra == "test"
+Requires-Dist: coverage-badge; extra == "test"
+Requires-Dist: cwltool; extra == "test"
+Requires-Dist: pylint>=2.15; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: pytest-order; extra == "test"
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pyyaml; extra == "test"
+Requires-Dist: pytest-requirements; extra == "test"
+Provides-Extra: doc
+Requires-Dist: linkify-it-py; extra == "doc"
+Requires-Dist: myst-parser; extra == "doc"
+Requires-Dist: nbsphinx; extra == "doc"
+Requires-Dist: numpydoc; extra == "doc"
+Requires-Dist: ctao-sphinx-theme; extra == "doc"
+Requires-Dist: sphinx-argparse; extra == "doc"
+Requires-Dist: sphinx-paramlinks; extra == "doc"
+Requires-Dist: sphinx>=8.2.1; extra == "doc"
+Requires-Dist: sphinx-changelog; extra == "doc"
+Provides-Extra: dev
+Requires-Dist: setuptools_scm; extra == "dev"
+Requires-Dist: towncrier; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Provides-Extra: all
+Requires-Dist: ctao-calibpipe[dev,doc,test]; extra == "all"
+Dynamic: license-file
+
+# DPPS Calibration Pipeline
+
+Welcome to `calibpipe` project. The project provides a selection of calibration tools
+for CTA raw data calibration. For full details see [project documentation][calibpipe-doc].
+
+## Installation
+
+### Installation for users
+
+Currently the package is under active development. First, create and activate a fresh conda environment:
+
+```
+mamba create -n calibpipe -c conda-forge python==3.12 ctapipe
+mamba activate calibpipe
+```
+and then install `calibpipe` using `pip` and TestPyPI:
+
+```
+pip install -i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ calibpipe
+```
+
+### Installation for developers
+
+## Contributing
+
+If you would like to contribute to this project please start from reading the [Contributing Guidelines][contributing].
+Then you can configure the project locally for development as outlined in the [Development Instructions][developing], and start to contribute.
+If you develop a new tool, don't forget to add a corresponding record to the `[project.scripts]` section of `pyproject.toml`
+
+Enjoy!
+
+[contributing]:http://cta-computing.gitlab-pages.cta-observatory.org/dpps/calibrationpipeline/calibpipe/latest/development/index.html
+[developing]:http://cta-computing.gitlab-pages.cta-observatory.org/dpps/calibrationpipeline/calibpipe/latest/getting_started/index.html#development-setup
+[calibpipe-doc]:http://cta-computing.gitlab-pages.cta-observatory.org/dpps/calibrationpipeline/calibpipe/latest/index.html