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pgdtools v0.1.0 (#43)
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* Refractor pgdtools

- remove proxy list
- move inner classes into individual files in their own folders
  - keep pgdtools.py cleaner
  - allow for keeping all files together cleaner
  - use imports in `__init__.py` in `sub_tools`
- Restructure tests to follow along with everything.

There are still a bunch of garbage routines in the files, these will need to be cleaned up next and stuff we don't want deleted.

* add nice reference treatment

* implement a bunch of dunder methods, cleaner style

* add techniques

Technique json file handling added, similar to how we handle the references.

* end of workday backup

* end of day backup

* finish filters

* add information class

* add a doctest and set xdoctests up in rye and CI

* add formatting class and start of data class. ratio can be returned already

* add ratio_xy routine for data getter. this also allows to get the correlation!

* Adding a first example, add capability to filter by reference and search refs

* add another example with Stephan et al. data for Mo

* stab at docs (API mainly)

* BF reset was in wrong spot

* fix typo, add a copy to not modify view of db

* fix techniques, update docs, add code of conduct

* bump version to 0.1.0

* update workflows to latest rye runner
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trappitsch authored Jul 26, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/pypi-publish.yml
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Expand Up @@ -15,7 +15,7 @@ jobs:
steps:
- uses: actions/checkout@v4
- name: Install the latest version of rye
uses: eifinger/setup-rye@v1
uses: eifinger/setup-rye@v4
- name: Sync Rye
run: |
rye sync --all-features
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6 changes: 4 additions & 2 deletions .github/workflows/tests.yml
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Expand Up @@ -27,13 +27,15 @@ jobs:
with:
python-version: ${{ matrix.python-version }}
- name: Install the latest version of rye
uses: eifinger/setup-rye@v3
uses: eifinger/setup-rye@v4
- name: Sync Rye
run: |
rye pin ${{ matrix.python-version }}
rye sync --all-features
- name: Run Tests for python interface
run: rye test
run: |
rye test
rye run test_docs
- name: Run Lint on one python
if: ${{ matrix.python-version == env.MAIN_PYTHON_VERSION }}
run: rye lint
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3 changes: 3 additions & 0 deletions .gitignore
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Expand Up @@ -55,3 +55,6 @@ htmlcov

## Jupyter
*.ipynb_checkpoints

## backup files
*.xlsx#
134 changes: 134 additions & 0 deletions CODE_OF_CONDUCT.md
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# Contributor Covenant Code of Conduct

## Our Pledge

We as members, contributors, and leaders pledge to make participation in our
community a harassment-free experience for everyone, regardless of age, body
size, visible or invisible disability, ethnicity, sex characteristics, gender
identity and expression, level of experience, education, socio-economic status,
nationality, personal appearance, race, caste, color, religion, or sexual
identity and orientation.

We pledge to act and interact in ways that contribute to an open, welcoming,
diverse, inclusive, and healthy community.

## Our Standards

Examples of behavior that contributes to a positive environment for our
community include:

* Demonstrating empathy and kindness toward other people
* Being respectful of differing opinions, viewpoints, and experiences
* Giving and gracefully accepting constructive feedback
* Accepting responsibility and apologizing to those affected by our mistakes,
and learning from the experience
* Focusing on what is best not just for us as individuals, but for the overall
community

Examples of unacceptable behavior include:

* The use of sexualized language or imagery, and sexual attention or advances of
any kind
* Trolling, insulting or derogatory comments, and personal or political attacks
* Public or private harassment
* Publishing others' private information, such as a physical or email address,
without their explicit permission
* Other conduct which could reasonably be considered inappropriate in a
professional setting

## Enforcement Responsibilities

Community leaders are responsible for clarifying and enforcing our standards of
acceptable behavior and will take appropriate and fair corrective action in
response to any behavior that they deem inappropriate, threatening, offensive,
or harmful.

Community leaders have the right and responsibility to remove, edit, or reject
comments, commits, code, wiki edits, issues, and other contributions that are
not aligned to this Code of Conduct, and will communicate reasons for moderation
decisions when appropriate.

## Scope

This Code of Conduct applies within all community spaces, and also applies when
an individual is officially representing the community in public spaces.
Examples of representing our community include using an official email address,
posting via an official social media account, or acting as an appointed
representative at an online or offline event.

## Enforcement

Instances of abusive, harassing, or otherwise unacceptable behavior may be
reported to the community leaders responsible for enforcement
via e-mail
(see [contact info](https://galactic-forensics.space/author/reto-trappitsch/)).
All complaints will be reviewed and investigated promptly and fairly.

All community leaders are obligated to respect the privacy and security of the
reporter of any incident.

## Enforcement Guidelines

Community leaders will follow these Community Impact Guidelines in determining
the consequences for any action they deem in violation of this Code of Conduct:

### 1. Correction

**Community Impact**: Use of inappropriate language or other behavior deemed
unprofessional or unwelcome in the community.

**Consequence**: A private, written warning from community leaders, providing
clarity around the nature of the violation and an explanation of why the
behavior was inappropriate. A public apology may be requested.

### 2. Warning

**Community Impact**: A violation through a single incident or series of
actions.

**Consequence**: A warning with consequences for continued behavior. No
interaction with the people involved, including unsolicited interaction with
those enforcing the Code of Conduct, for a specified period of time. This
includes avoiding interactions in community spaces as well as external channels
like social media. Violating these terms may lead to a temporary or permanent
ban.

### 3. Temporary Ban

**Community Impact**: A serious violation of community standards, including
sustained inappropriate behavior.

**Consequence**: A temporary ban from any sort of interaction or public
communication with the community for a specified period of time. No public or
private interaction with the people involved, including unsolicited interaction
with those enforcing the Code of Conduct, is allowed during this period.
Violating these terms may lead to a permanent ban.

### 4. Permanent Ban

**Community Impact**: Demonstrating a pattern of violation of community
standards, including sustained inappropriate behavior, harassment of an
individual, or aggression toward or disparagement of classes of individuals.

**Consequence**: A permanent ban from any sort of public interaction within the
community.

## Attribution

This Code of Conduct is adapted from the [Contributor Covenant][homepage],
version 2.1, available at
[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].

Community Impact Guidelines were inspired by
[Mozilla's code of conduct enforcement ladder][Mozilla CoC].

For answers to common questions about this code of conduct, see the FAQ at
[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
[https://www.contributor-covenant.org/translations][translations].

[homepage]: https://www.contributor-covenant.org
[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
[Mozilla CoC]: https://github.com/mozilla/diversity
[FAQ]: https://www.contributor-covenant.org/faq
[translations]: https://www.contributor-covenant.org/translations
5 changes: 3 additions & 2 deletions README.md
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@@ -1,9 +1,10 @@
[![PyPi](https://img.shields.io/pypi/v/pgdtools?color=informational)](https://pypi.org/project/pgdtools/)
[![docs](https://readthedocs.org/projects/pgdtools/badge/?version=latest)](https://pgdtools.readthedocs.io)
[![License](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/NASA-Planetary-Science/pgdtools/blob/main/LICENSE)
[![tests](https://github.com/NASA-Planetary-Science/pgdtools/actions/workflows/rimseval_testing.yml/badge.svg?branch=main)](https://github.com/NASA-Planetary-Science/pgdtools/)
[![tests](https://github.com/NASA-Planetary-Science/pgdtools/actions/workflows/tests.yml/badge.svg)](https://github.com/NASA-Planetary-Science/pgdtools/actions/workflows/tests.yml)
[![codecov](https://codecov.io/gh/NASA-Planetary-Science/pgdtools/branch/main/graph/badge.svg?token=N0NNVEI8CX)](https://codecov.io/gh/NASA-Planetary-Science/pgdtools)
[![Style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
[![Rye](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/rye/main/artwork/badge.json)](https://rye.astral.sh)
[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](code_of_conduct.md)

# Presolar grain database tools (pgdTools)

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5 changes: 5 additions & 0 deletions docs/api/classify.md
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# Classify your own data

::: pgdtools.classify
options:
members: null
8 changes: 8 additions & 0 deletions docs/api/db.md
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# Database

Details on database management can be found
[here](../users/db.md).

::: pgdtools.db.config
options:
members: null
7 changes: 7 additions & 0 deletions docs/api/maintainer.md
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# Maintainer tools

A detailed walk-through for maintainers can be found in the maintainer user guide.

::: pgdtools.maintainer
options:
members: null
21 changes: 21 additions & 0 deletions docs/api/pgdtools.md
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# PGDTools

In here is the main class `PresolarGrains`.
You can either load this class either by importing and defining it:

```python
from pgdtools import PresolarGrains
pgd = PresolarGrains()
```

or by importing the `pgd` command directly:

```python
from pgdtools import pgd
```

Most functionality is available through the available [subtools](subtools.md).

::: pgdtools.pgdtools
options:
members: null
28 changes: 28 additions & 0 deletions docs/api/subtools.md
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@@ -0,0 +1,28 @@
# PGD Subtools

These are subtools for the `PresolarGrains` class.
All of them must be invoked from the `PresolarGrains` class!

::: pgdtools.sub_tools.data
options:
members: null

::: pgdtools.sub_tools.filters
options:
members: null

::: pgdtools.sub_tools.format
options:
members: null

::: pgdtools.sub_tools.info
options:
members: null

::: pgdtools.sub_tools.references
options:
members: null

::: pgdtools.sub_tools.techniques
options:
members: null
134 changes: 134 additions & 0 deletions docs/code_of_conduct.md
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@@ -0,0 +1,134 @@

# Contributor Covenant Code of Conduct

## Our Pledge

We as members, contributors, and leaders pledge to make participation in our
community a harassment-free experience for everyone, regardless of age, body
size, visible or invisible disability, ethnicity, sex characteristics, gender
identity and expression, level of experience, education, socio-economic status,
nationality, personal appearance, race, caste, color, religion, or sexual
identity and orientation.

We pledge to act and interact in ways that contribute to an open, welcoming,
diverse, inclusive, and healthy community.

## Our Standards

Examples of behavior that contributes to a positive environment for our
community include:

* Demonstrating empathy and kindness toward other people
* Being respectful of differing opinions, viewpoints, and experiences
* Giving and gracefully accepting constructive feedback
* Accepting responsibility and apologizing to those affected by our mistakes,
and learning from the experience
* Focusing on what is best not just for us as individuals, but for the overall
community

Examples of unacceptable behavior include:

* The use of sexualized language or imagery, and sexual attention or advances of
any kind
* Trolling, insulting or derogatory comments, and personal or political attacks
* Public or private harassment
* Publishing others' private information, such as a physical or email address,
without their explicit permission
* Other conduct which could reasonably be considered inappropriate in a
professional setting

## Enforcement Responsibilities

Community leaders are responsible for clarifying and enforcing our standards of
acceptable behavior and will take appropriate and fair corrective action in
response to any behavior that they deem inappropriate, threatening, offensive,
or harmful.

Community leaders have the right and responsibility to remove, edit, or reject
comments, commits, code, wiki edits, issues, and other contributions that are
not aligned to this Code of Conduct, and will communicate reasons for moderation
decisions when appropriate.

## Scope

This Code of Conduct applies within all community spaces, and also applies when
an individual is officially representing the community in public spaces.
Examples of representing our community include using an official email address,
posting via an official social media account, or acting as an appointed
representative at an online or offline event.

## Enforcement

Instances of abusive, harassing, or otherwise unacceptable behavior may be
reported to the community leaders responsible for enforcement
via e-mail
(see [contact info](https://galactic-forensics.space/author/reto-trappitsch/)).
All complaints will be reviewed and investigated promptly and fairly.

All community leaders are obligated to respect the privacy and security of the
reporter of any incident.

## Enforcement Guidelines

Community leaders will follow these Community Impact Guidelines in determining
the consequences for any action they deem in violation of this Code of Conduct:

### 1. Correction

**Community Impact**: Use of inappropriate language or other behavior deemed
unprofessional or unwelcome in the community.

**Consequence**: A private, written warning from community leaders, providing
clarity around the nature of the violation and an explanation of why the
behavior was inappropriate. A public apology may be requested.

### 2. Warning

**Community Impact**: A violation through a single incident or series of
actions.

**Consequence**: A warning with consequences for continued behavior. No
interaction with the people involved, including unsolicited interaction with
those enforcing the Code of Conduct, for a specified period of time. This
includes avoiding interactions in community spaces as well as external channels
like social media. Violating these terms may lead to a temporary or permanent
ban.

### 3. Temporary Ban

**Community Impact**: A serious violation of community standards, including
sustained inappropriate behavior.

**Consequence**: A temporary ban from any sort of interaction or public
communication with the community for a specified period of time. No public or
private interaction with the people involved, including unsolicited interaction
with those enforcing the Code of Conduct, is allowed during this period.
Violating these terms may lead to a permanent ban.

### 4. Permanent Ban

**Community Impact**: Demonstrating a pattern of violation of community
standards, including sustained inappropriate behavior, harassment of an
individual, or aggression toward or disparagement of classes of individuals.

**Consequence**: A permanent ban from any sort of public interaction within the
community.

## Attribution

This Code of Conduct is adapted from the [Contributor Covenant][homepage],
version 2.1, available at
[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].

Community Impact Guidelines were inspired by
[Mozilla's code of conduct enforcement ladder][Mozilla CoC].

For answers to common questions about this code of conduct, see the FAQ at
[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
[https://www.contributor-covenant.org/translations][translations].

[homepage]: https://www.contributor-covenant.org
[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
[Mozilla CoC]: https://github.com/mozilla/diversity
[FAQ]: https://www.contributor-covenant.org/faq
[translations]: https://www.contributor-covenant.org/translations
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