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3 changes: 3 additions & 0 deletions .github/CONTRIBUTING.md
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Expand Up @@ -15,6 +15,9 @@ If you want to open an issue, make sure to follow these steps:

Nice to see that you are interested in contributing to our code! Here is a general workflow for contributing to our project.

>[!NOTE]
>We are a privacy-focused project which thrives on trust and accountability. Therefore, we __do not allow any GenAI__ in this repository.

1. Add an [issue](https://github.com/sodascience/metasyn/issues) describing the feature you want to add, or comment on an existing issue that you want to try solving it. The goal of this is to prevent you from spending time working on things that will not be accepted into our project. In general, we like to have some discussion on our issues before we start programming.
2. Fork the project and create a new branch on your fork (e.g., `add-cool-feature`)
3. Code the code 💻
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2 changes: 1 addition & 1 deletion .github/workflows/core-ci.yml
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Expand Up @@ -76,7 +76,7 @@ jobs:
run: |
metasyn schema -o current_schema.json
MD5_DATA=(`md5sum current_schema.json`)
[[ ${MD5_DATA[0]} == "8e9351c9b1513a6586ad94fa8b82d94e" ]]
[[ ${MD5_DATA[0]} == "95a44bdef1e929e718a2c9647795b147" ]]



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4 changes: 2 additions & 2 deletions .readthedocs.yaml
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Expand Up @@ -7,7 +7,7 @@ version: 2

# Set the version of Python and other tools you might need
build:
os: ubuntu-20.04
os: ubuntu-24.04
tools:
python: "3.12"
#
Expand All @@ -21,4 +21,4 @@ python:
- method: pip
path: .
extra_requirements:
- docs
- docs
72 changes: 72 additions & 0 deletions docs/source/_templates/autosummary/module.rst
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@@ -0,0 +1,72 @@
{{ fullname | escape | underline}}

.. automodule:: {{ fullname }}

{% if modules %}
.. rubric:: Submodules

.. autosummary::
:toctree:
{% for item in modules %}
{{ item }}
{%- endfor %}
{% endif %}

{% if attributes %}
.. rubric:: Module Attributes

.. autosummary::
{% for item in attributes %}
{{ item }}
{%- endfor %}

{% for item in attributes %}
.. autodata:: {{ item }}
:no-index:
{% endfor %}
{% endif %}

{% if functions %}
.. rubric:: Functions

.. autosummary::
{% for item in functions %}
{{ item }}
{%- endfor %}

{% for item in functions %}
.. autofunction:: {{ item }}
:no-index:
{% endfor %}
{% endif %}

{% if classes %}
.. rubric:: Classes

.. autosummary::
{% for item in classes %}
{{ item }}
{%- endfor %}

{% for item in classes %}
.. autoclass:: {{ item }}
:members:
:show-inheritance:
:no-index:

{% endfor %}
{% endif %}

{% if exceptions %}
.. rubric:: Exceptions

.. autosummary::
{% for item in exceptions %}
{{ item }}
{%- endfor %}

{% for item in exceptions %}
.. autoexception:: {{ item }}
:no-index:
{% endfor %}
{% endif %}
10 changes: 0 additions & 10 deletions docs/source/api/demo.rst

This file was deleted.

137 changes: 54 additions & 83 deletions docs/source/api/developer_reference.rst
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@@ -1,86 +1,57 @@
Developer reference
===================

This section is intended for those that want to contribute to the metasyn package, or simply want a deeper understanding of how it works. It contains the classes, functions and modules that are not in the rest of the reference API. These are mostly elements that are not directly used by users, but are important for developers of the metasyn package to understand the architecture.

DistSpec
^^^^^^^^

.. autoclass:: metasyn.varspec.DistributionSpec
:members:
:undoc-members:
:show-inheritance:

metasyn.config module
^^^^^^^^^^^^^^^^^^^^^

.. automodule:: metasyn.config
:members:
:undoc-members:
:show-inheritance:


metasyn.registry module
^^^^^^^^^^^^^^^^^^^^^^^

.. automodule:: metasyn.registry
:members:
:undoc-members:
:show-inheritance:

metasyn.var module
^^^^^^^^^^^^^^^^^^

.. automodule:: metasyn.var
:members:
:undoc-members:
:show-inheritance:

metasyn.testutils module
^^^^^^^^^^^^^^^^^^^^^^^^

.. automodule:: metasyn.testutils
:members:
:undoc-members:
:show-inheritance:

metasyn.validation module
^^^^^^^^^^^^^^^^^^^^^^^^^

.. automodule:: metasyn.validation
:members:
:undoc-members:
:show-inheritance:

metasyn.privacy module
^^^^^^^^^^^^^^^^^^^^^^

.. automodule:: metasyn.privacy
:members:
:undoc-members:
:show-inheritance:

metasyn.util module
^^^^^^^^^^^^^^^^^^^

.. automodule:: metasyn.util
:members:
:undoc-members:
:show-inheritance:

metasyn.file module
^^^^^^^^^^^^^^^^^^^
.. automodule:: metasyn.file
:members:
:private-members:
:undoc-members:
:show-inheritance:

metasyn.distribution.base module
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. automodule:: metasyn.distribution.base
:members:
:show-inheritance:
:private-members:

This section is intended for those that want to contribute to the metasyn package, or simply want a deeper understanding of how it works. It contains all the classes, functions and modules in the metasyn package. Most elements are not directly used by users, but are important for developers of the metasyn package to understand the architecture.

.. currentmodule:: metasyn

Modules
-------

.. autosummary::
:toctree: generated
:recursive:

config
demo
distribution
file
metaframe
privacy
registry
schema
testutils
util
validation
var
varspec

Top-level classes
-----------------

.. autosummary::
:toctree: generated

MetaFrame
MetaVar
VarSpec

Top-level functions
-------------------

.. autosummary::
:toctree: generated

demo_dataframe
demo_file
metadist
read_csv
read_dta
read_excel
read_sav
read_tsv
write_csv
write_dta
write_excel
write_sav
write_tsv
1 change: 1 addition & 0 deletions docs/source/api/metaframe.rst
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Expand Up @@ -5,3 +5,4 @@ MetaFrame
:members:
:undoc-members:
:show-inheritance:
:no-index:
1 change: 1 addition & 0 deletions docs/source/api/metasyn.demo.rst
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Expand Up @@ -8,3 +8,4 @@ Demonstration datasets
:inherited-members:
:private-members:
:show-inheritance:
:no-index:
1 change: 1 addition & 0 deletions docs/source/api/metasyn.rst
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Expand Up @@ -10,5 +10,6 @@ This section aims to give an overview of all classes, functions and methods in t
metasyn.demo
metaframe
varspec
multiframe
developer_reference

7 changes: 7 additions & 0 deletions docs/source/api/multiframe.rst
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@@ -0,0 +1,7 @@
Multiframe
==========

.. automodule:: metasyn.multiframe
:members:
:undoc-members:
:show-inheritance:
1 change: 1 addition & 0 deletions docs/source/api/varspec.rst
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Expand Up @@ -6,4 +6,5 @@ VarSpec
:members:
:undoc-members:
:show-inheritance:
:no-index:

8 changes: 4 additions & 4 deletions docs/source/cli.rst
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Expand Up @@ -73,27 +73,27 @@ Here's how you can use Docker to access Metasyn's CLI:


.. note::
You can also specify which ``metasyn`` version to use in docker, by adding a tag to the docker image. For example, to use version 1.1.0, you can use the following command:
You can also specify which ``metasyn`` version to use in docker, by adding a tag to the docker image. For example, to use version 2.1.0, you can use the following command:

.. tab:: Installing a specific version

.. code-block:: console

docker pull sodateam/metasyn:v1.1.0
docker pull sodateam/metasyn:v2.1.0

.. tab:: Using a command on a specific version

.. tab:: Windows

.. code-block:: console

docker run -v %cd%:/wd sodateam/metasyn:v1.1.0 --help
docker run -v %cd%:/wd sodateam/metasyn:v2.1.0 --help

.. tab:: Unix or MacOS:

.. code-block:: console

docker run -v $(pwd):/wd sodateam/metasyn:v1.1.0 --help
docker run -v $(pwd):/wd sodateam/metasyn:v2.1.0 --help


Creating generative metadata
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4 changes: 2 additions & 2 deletions docs/source/conf.py
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Expand Up @@ -25,7 +25,7 @@


# The full version, including alpha/beta/rc tags
release = '2.0.0'
release = '2.1.0'

# -- General configuration ---------------------------------------------------

Expand Down Expand Up @@ -66,7 +66,7 @@
html_theme_options = {
"logo_only": True,
"navigation_depth": -1,
"display_version": True,
"version_selector": True,
"style_external_links": False,
}

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1 change: 1 addition & 0 deletions docs/source/index.rst
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Expand Up @@ -47,6 +47,7 @@ for data owners to share the structure and approximation of the content of their

improve_synth
datafree
multiframe

.. toctree::
:hidden:
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