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Prepare first upload to PyPI #107

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Mar 5, 2021
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Prepare first upload to PyPI #107

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701c05d
update gitignore
HealthyPear Mar 1, 2021
b36ca7b
update setup.py
HealthyPear Mar 1, 2021
c18f222
bump version
HealthyPear Mar 1, 2021
1a9018b
Update zenodo JSON
HealthyPear Mar 2, 2021
4c2f396
Update README
HealthyPear Mar 2, 2021
6d1145a
Update installation instructions
HealthyPear Mar 2, 2021
e5c8091
Bump version
HealthyPear Mar 2, 2021
f157b9a
Remove metadata keyword
HealthyPear Mar 2, 2021
4e5a811
fix indentation (probably harmless)
HealthyPear Mar 2, 2021
2c9492d
Update .zenodo.json
HealthyPear Mar 3, 2021
a82f151
Remove jupyterlab and vitables from installation requirements and update
HealthyPear Mar 5, 2021
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3 changes: 2 additions & 1 deletion .gitignore
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Expand Up @@ -11,7 +11,8 @@
__pycache__

# ignore version cache file (generated automatically when setup.py is run)
ctapipe/_version_cache.py
protopipe/_version_cache.py
protopipe/_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`.
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8 changes: 3 additions & 5 deletions .zenodo.json
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{
"metadata": {
"title" : "protopipe",
"description": "A ctapipe-based pipeline prototype for the Cherenkov Telescope Array (CTA).",
"description": "Pipeline prototype for the Cherenkov Telescope Array (CTA).",
"license": {
"id": "CECILL-B"
},
"version": "v0.4.0",
"doi": "10.5281/zenodo.4303995",
"keywords": [
"gamma-ray astronomy",
"Imaging Atmospheric Cherenkov Telescope",
Expand Down Expand Up @@ -66,6 +65,5 @@
"type": "Other",
"name": "Garcia, Enrique"
}
]
]
}
}
17 changes: 10 additions & 7 deletions README.rst
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@@ -1,6 +1,6 @@
==================================================
protopipe |CI| |codacy| |coverage| |documentation|
==================================================
==============================================================
protopipe |CI| |codacy| |coverage| |documentation| |doilatest|
==============================================================

.. |CI| image:: https://github.com/cta-observatory/protopipe/workflows/CI/badge.svg?branch=master
:target: https://github.com/cta-observatory/protopipe/actions?query=workflow%3ACI
Expand All @@ -10,7 +10,9 @@ protopipe |CI| |codacy| |coverage| |documentation|
:target: https://codecov.io/gh/cta-observatory/protopipe
.. |documentation| image:: https://readthedocs.org/projects/protopipe/badge/?version=latest
:target: https://protopipe.readthedocs.io/en/latest/?badge=latest
.. |doilatest| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4303996.svg
.. |doilatest| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4303995.svg
:target: https://doi.org/10.5281/zenodo.4303995
.. |doi_v0.3.0| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4303996.svg
:target: https://doi.org/10.5281/zenodo.4303996

A pipeline prototype for the `Cherenkov Telescope Array (CTA) <www.cta-observatory.org>`_.
Expand All @@ -28,6 +30,7 @@ Resources
- Current performance: `RedMine <https://forge.in2p3.fr/projects/benchmarks-reference-analysis/wiki/Protopipe_performance_data>`__

- Slack channels:

- `#protopipe <https://cta-aswg.slack.com/archives/CPTN4U7U7>`__
- `#protopipe_github <https://cta-aswg.slack.com/archives/CPUSPPHST>`__
- `#protopipe-grid <https://cta-aswg.slack.com/archives/C01FWH8E0TT>`__
Expand All @@ -38,7 +41,7 @@ Citing this software
If you use a released version of this software for a publication,
please cite it by using the corresponding DOI.

Please, check the development version of this file for up-to-date links.

- v0.3.0 : |doilatest|
- latest : |doilatest|
- v0.4.0 : TBD
- v0.3.0 : |doi_v0.3.0|

13 changes: 6 additions & 7 deletions docs/install/development.rst
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Expand Up @@ -4,15 +4,14 @@ Development version
===================

1. `fork <https://help.github.com/en/articles/fork-a-repo>`__ the `repository <https://github.com/cta-observatory/protopipe>`_
2. ``conda env create -f environment.yml``
3. ``conda activate protopipe``
4. ``pip install -e .``

In this way, you will always use the version of the source code on which you
are working.
2. create and enter a basic virtual environment (or use the ``environment.yaml`` file)
3. ``pip install -e '.[all]'``

The ``all`` keyword will install all extra requirements,
which can be also installed separately using ``tests`` and ``docs``.

Next steps:

* get accustomed to the basic pipeline workflow (:ref:`use-pipeline`),
* make your own complete analysis (:ref:`use-grid`),
* for bugs and new features, please contribute to the project (:ref:`contribute`).
* learn how to contribute to the project (:ref:`contribute`).
22 changes: 14 additions & 8 deletions docs/install/index.rst
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Installation
============

The only requirement is an Anaconda (or Miniconda) installation which supports
Python 3.
Requirements:

There are two different ways to install `protopipe`,
- ``Python >= 3.7``
- ``pip``

* if you just want to use it as it is (:ref:`install-release`),
* or if you also want to develop it (:ref:`install-development`).
It is recommended to work within a virtual environment, using for example
``venv`` or Anaconda's ``conda``.

.. note::
For both types of installation the use of `mamba <https://github.com/mamba-org/mamba#readme>`__
might provide improved speed during the creation of the `conda` environment.
In case you want to use Anaconda it is recommended to use
`mamba <https://github.com/mamba-org/mamba#readme>`__
for improved speed during the creation of the virtual environment.

There are two different ways to install ``protopipe``,

* if you just want to use it as it is (:ref:`install-release`),
* or if you also want to develop it (:ref:`install-development`).

In both cases, if you want to perform a full analysis, you will need some
computational power in order to produce enough
data files for model and performance estimation.
This can be accomplished through the use of a GRID environment.

After installing `protopipe`,
After installing ``protopipe``,

* install the code necessary to interface it with the grid (:ref:`install-grid`),
* use protopipe on the grid (:ref:`use-grid`).
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16 changes: 11 additions & 5 deletions docs/install/release.rst
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Released version
================

1. download the `latest released version <https://github.com/cta-observatory/protopipe/releases>`__
2. ``cd protopipe-X.Y.Z``
3. ``conda env create -f environment.yml -n protopipe-X.Y.Z``
4. ``conda activate protopipe``
5. ``pip install .``
You can find all released versions .

To install a released version >= ``0.4.0`` it is sufficient to install the
package from ``PyPI`` with ``pip install protopipe``.

For previous releases,

1. download the corresponding tarball stored `here <https://github.com/cta-observatory/protopipe/releases>`__
2. ``conda env create -f environment.yml -n protopipe-X.Y.Z``
3. ``conda activate protopipe-X.Y.Z``
4. ``pip install .``

Next steps:

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2 changes: 1 addition & 1 deletion protopipe/__init__.py
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__version__ = "0.4.0-dev"
__version__ = "0.4.0.post1"
3 changes: 2 additions & 1 deletion setup.py
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Expand Up @@ -25,6 +25,7 @@ def readme():
"pytest",
"pytest-cov",
"codecov",
"ctapipe-extra @ https://github.com/cta-observatory/ctapipe-extra/archive/v0.3.1.tar.gz",
],
}

Expand All @@ -42,7 +43,7 @@ def readme():
packages=find_packages(),
package_data={"protopipe": ["aux/example_config_files/protopipe/analysis.yaml"]},
include_package_data=True,
install_requires=["ctapipe"],
install_requires=["ctapipe==0.9.1", "jupyterlab", "pyirf", "vitables"],
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@kosack kosack Mar 2, 2021 •
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is jupyterlab and vitables really required? or only to generate docs? install_requires should only be things that are required to run, not useful things in the user's environment (which would go into environment.yml, or similar). I think the only requirements should be ctapipe and pyirf.

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This is for a pure pip installation, so after pip install protopipe the user should have all the necessary tools to use protopipe and like this it doesn't really need even conda.
For now "use protopipe" means also benchmarking and checking data, so for me these 2 tools are necessary for the package as a whole.

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@kosack kosack Mar 5, 2021 •
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I think that is the incorrect way to do it. Pip is not meant for making environments, only for installing required dependencies. For environments you need to use pipenv or poetry, or just provide a requirements.txt file that is the output of pip freeze. In the package itself (in setup.py) you should only list the bare minimum to allow it to work. Otherwise you will run into dependency resolution problems later.

So here you should have only ctapipe and pyirf as dependencies.

For reference: https://packaging.python.org/discussions/install-requires-vs-requirements/:

Whereas install_requires requirements are minimal, requirements files often contain an exhaustive listing of pinned versions for the purpose of achieving repeatable installations of a complete environment.

zip_safe=False,
extras_require={
"all": extras_require["all"],
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