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Journal of Open Source Science paper #35

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Jan 17, 2025
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3d993df
test_github_editor_md_preview
erialC-P Nov 27, 2024
953f8df
Basic paper framework
erialC-P Nov 27, 2024
466bca4
statement of need draft
erialC-P Nov 28, 2024
fa3a2db
update to statement of need draft
erialC-P Nov 28, 2024
e3d71ae
Summary draft
erialC-P Nov 28, 2024
0feacd4
Summary draft
erialC-P Nov 28, 2024
b97bb97
formatting
erialC-P Nov 28, 2024
5308ef0
restructure and review
erialC-P Nov 29, 2024
1d5f595
move to new paper subfolder
erialC-P Nov 29, 2024
03a25c4
early Functionality section drafting
erialC-P Nov 29, 2024
2d0e2de
Test adding Github action
robbibt Nov 29, 2024
ffcd51c
Update path
robbibt Nov 29, 2024
c8abc7e
Only run on specific files and branches
robbibt Nov 29, 2024
0a3a571
early Functionality section drafting
erialC-P Nov 29, 2024
b9b3f21
Draft functionality
erialC-P Dec 2, 2024
68eef70
draft tide biases section
erialC-P Dec 2, 2024
0f78f86
draft validation section
erialC-P Dec 2, 2024
97193fd
Full draft reviews
erialC-P Dec 2, 2024
29b29fe
Bib testing
erialC-P Dec 2, 2024
355b751
bib update
erialC-P Dec 2, 2024
c97ef5b
bib update
erialC-P Dec 2, 2024
0acab9d
referencing update
erialC-P Dec 2, 2024
049bfd6
bib testing
erialC-P Dec 3, 2024
4be9dd1
bib test
erialC-P Dec 3, 2024
389a70a
bib updates
erialC-P Dec 3, 2024
e5fac5c
reference updates, figure labelling test
erialC-P Dec 3, 2024
97879ee
fig labelling test
erialC-P Dec 3, 2024
20f7b01
fig label test
erialC-P Dec 3, 2024
18efdfd
fig test
erialC-P Dec 3, 2024
fa7d869
sen2 tide stats image and bib update
erialC-P Dec 3, 2024
e7e78a8
edited figure, full draft
erialC-P Dec 3, 2024
6b1af81
minor formatting
erialC-P Dec 3, 2024
ed2d6b6
removed fake yaml section
erialC-P Dec 3, 2024
05aaaa5
formatting
erialC-P Dec 3, 2024
47d3179
Review and minor restructure
erialC-P Dec 5, 2024
92c3958
review and restructure
erialC-P Dec 6, 2024
79b9719
yaml reformatting
erialC-P Dec 6, 2024
eb037e5
formatting
erialC-P Dec 6, 2024
f6b82b7
bib formatting
erialC-P Dec 6, 2024
2a2e810
JOSS paper draft edits (#34)
robbibt Dec 13, 2024
a5121f4
Fix formatting
robbibt Dec 13, 2024
3a3e848
Reocate to top level
robbibt Dec 13, 2024
6c8a0a6
Fix multiple packages
robbibt Dec 13, 2024
f1d72c7
Second attempt
robbibt Dec 13, 2024
33767c8
Update action ignored files
robbibt Dec 13, 2024
7a273f7
Add draft PDF
robbibt Dec 13, 2024
3b68ab3
Small update
robbibt Dec 13, 2024
a30be13
Add gesla figure
robbibt Dec 13, 2024
68af37e
Update paper
robbibt Dec 13, 2024
f799818
Add timeout
robbibt Dec 13, 2024
61951b9
add `pyTMD` blurbs to paper.md (#38)
tsutterley Jan 13, 2025
d673692
Add comment bot
robbibt Jan 13, 2025
8580cf7
Update paper.yml
robbibt Jan 13, 2025
187cada
Update paper.yml
robbibt Jan 13, 2025
b6afd13
Update paper.yml
robbibt Jan 13, 2025
4c123cd
Update paper.yml
robbibt Jan 13, 2025
038fa35
Update paper.yml
robbibt Jan 13, 2025
43987c8
Create paper-comment.yml
robbibt Jan 13, 2025
1586650
Update paper-comment.yml
robbibt Jan 13, 2025
ff3f256
Update paper.yml
robbibt Jan 13, 2025
a65fa82
Update paper.yml
robbibt Jan 13, 2025
5004b7f
Try commiting updated PDF
robbibt Jan 13, 2025
789b352
Update generated PDF
robbibt Jan 13, 2025
1558d27
Update modelling tides section
robbibt Jan 13, 2025
20db2d0
Update generated PDF
robbibt Jan 13, 2025
9c2736b
Add table
robbibt Jan 13, 2025
5b3624b
Update generated PDF
robbibt Jan 13, 2025
ee934f6
Update table with dummy data
robbibt Jan 13, 2025
b77c55a
Update generated PDF
robbibt Jan 13, 2025
f219fa5
Use correct values for 32 cores
robbibt Jan 13, 2025
6cd6350
Update generated PDF
robbibt Jan 13, 2025
ad10bc9
Fix docstrings
robbibt Jan 13, 2025
2f85898
Merge branch 'main' into JOSS_paper
robbibt Jan 13, 2025
e169a83
Update generated PDF
robbibt Jan 13, 2025
b8b6686
Add citation
robbibt Jan 13, 2025
e9a6407
Update generated PDF
robbibt Jan 13, 2025
f374394
Update wording, use real values for timing
robbibt Jan 13, 2025
0457eb6
Update generated PDF
robbibt Jan 13, 2025
4b07de3
Decimal places
robbibt Jan 13, 2025
86114b1
Update generated PDF
robbibt Jan 13, 2025
ed935c7
Fix formatting
robbibt Jan 13, 2025
cd04f25
Update generated PDF
robbibt Jan 13, 2025
234b904
Format refs
robbibt Jan 13, 2025
d2de300
Update generated PDF
robbibt Jan 13, 2025
e64580c
Wording
robbibt Jan 13, 2025
7bfe229
Update generated PDF
robbibt Jan 13, 2025
1281f2f
Edit citation format
robbibt Jan 13, 2025
8e6c789
Update generated PDF
robbibt Jan 13, 2025
88cdb94
Minor updates
robbibt Jan 13, 2025
bc5dd36
Update citation
robbibt Jan 14, 2025
ca10665
Update generated PDF
robbibt Jan 14, 2025
0e6ebb2
Add additional citations
robbibt Jan 14, 2025
a7de907
Update generated PDF
robbibt Jan 14, 2025
e7a5ae3
Minor wording
robbibt Jan 14, 2025
021f34d
Wording
robbibt Jan 14, 2025
56f5e45
Update generated PDF
robbibt Jan 14, 2025
5a29c06
Minor wording
robbibt Jan 14, 2025
a3bf564
Update generated PDF
robbibt Jan 14, 2025
a894e4b
Wording
robbibt Jan 14, 2025
4cb95f1
Update generated PDF
robbibt Jan 14, 2025
8589374
Wording
robbibt Jan 14, 2025
131fa34
Update generated PDF
robbibt Jan 14, 2025
4d4063a
Update readmes, formatting
robbibt Jan 14, 2025
b07ab70
Update generated PDF
robbibt Jan 14, 2025
d370e2c
Update readme
robbibt Jan 14, 2025
dd57989
Update generated PDF
robbibt Jan 14, 2025
ad9d11a
Update readme
robbibt Jan 14, 2025
f1e8d24
Merge branch 'JOSS_paper' of https://github.com/GeoscienceAustralia/e…
robbibt Jan 14, 2025
3a38194
Readme
robbibt Jan 14, 2025
460a486
Update generated PDF
robbibt Jan 14, 2025
86b01dd
Update contributing
robbibt Jan 14, 2025
ff5086f
Merge branch 'JOSS_paper' of https://github.com/GeoscienceAustralia/e…
robbibt Jan 14, 2025
a27590a
Update generated PDF
robbibt Jan 14, 2025
7be04da
Update benchmarking, add title
robbibt Jan 14, 2025
03fabff
Update generated PDF
robbibt Jan 14, 2025
1c523fb
Add copyright
robbibt Jan 14, 2025
d82d412
Update generated PDF
robbibt Jan 14, 2025
0a3c1ea
Minor wording
robbibt Jan 14, 2025
992e56d
Merge branch 'JOSS_paper' of https://github.com/GeoscienceAustralia/e…
robbibt Jan 14, 2025
9dd0c4b
Update generated PDF
robbibt Jan 14, 2025
b18d6ab
Add Africa to research projects
robbibt Jan 14, 2025
e3fd96f
Merge branch 'JOSS_paper' of https://github.com/GeoscienceAustralia/e…
robbibt Jan 14, 2025
5a59ce0
Update generated PDF
robbibt Jan 14, 2025
1d4c70a
Formatting
robbibt Jan 14, 2025
dc65719
Update generated PDF
robbibt Jan 14, 2025
d59dd5e
Update paper.md
robbibt Jan 16, 2025
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robbibt Jan 16, 2025
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6 changes: 6 additions & 0 deletions .github/workflows/main.yml
Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,14 @@ on:
push:
branches:
- main
paths-ignore:
- "paper/**"
- "README.md"
pull_request:
types: [opened, synchronize, reopened]
paths-ignore:
- "paper/**"
- "README.md"

env:
EO_TIDES_TIDE_MODELS: ./tests/data/tide_models
Expand Down
47 changes: 47 additions & 0 deletions .github/workflows/paper.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,47 @@
name: Draft paper PDF
on:
push:
branches:
- main
- JOSS_paper
paths:
- paper/**
- .github/workflows/paper.yml
pull_request:
branches:
- main
- JOSS_paper
paths:
- paper/**
- .github/workflows/paper.yml

jobs:
paper:
runs-on: ubuntu-latest
name: Generate paper draft
steps:
- name: Checkout
uses: actions/checkout@v4

- name: Build draft PDF
uses: openjournals/openjournals-draft-action@master
with:
journal: joss
paper-path: paper/paper.md

- name: Upload
uses: actions/upload-artifact@v4
with:
name: paper
# Output path where Pandoc will write the compiled PDF.
# Note, this should be the same directory as the input
# paper.md
path: paper/paper.pdf

- name: Commit updated PDF
uses: stefanzweifel/git-auto-commit-action@v4
if: github.event_name == 'pull_request'
continue-on-error: true
with:
commit_message: Update generated PDF
file_pattern: "paper/paper.pdf"
22 changes: 1 addition & 21 deletions CONTRIBUTING.md
Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
# Contributing to `eo-tides`

Contributions are welcome, and they are greatly appreciated!
Every little bit helps, and credit will always be given.

You can contribute in many ways:

Expand Down Expand Up @@ -92,17 +91,7 @@ Now, validate that all unit tests are passing:
make test
```

9. Before raising a pull request you can also run tox to
run the tests across different versions of Python:

```bash
tox
```

This requires you to have multiple versions of python installed.
This step is also triggered in the CI/CD pipeline, so you could also choose to skip this step locally.

10. Commit your changes and push your branch to GitHub:
9. Commit your changes and push your branch to GitHub:

```bash
git add .
Expand All @@ -111,12 +100,3 @@ git push origin name-of-your-bugfix-or-feature
```

11. Submit a pull request through the GitHub website.

# Pull Request Guidelines

Before you submit a pull request, check that it meets these guidelines:

1. The pull request should ideally include tests.

2. If the pull request adds functionality, the docs should be updated.
Put your new functionality into a function with a docstring, and add the feature to the list in `README.md`.
3 changes: 1 addition & 2 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -12,8 +12,7 @@
- 📘 **Documentation**: <https://GeoscienceAustralia.github.io/eo-tides/>
- 🐍 **PyPI**: <https://pypi.org/project/eo-tides/>

> [!CAUTION]
> This package is a work in progress, and not currently ready for operational use.
<br>

`eo-tides` provides powerful parallelized tools for integrating satellite Earth observation data with tide modelling. 🛠️🌊🛰️

Expand Down
Binary file modified docs/assets/eo-tides-abstract.gif
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4 changes: 0 additions & 4 deletions docs/index.md
Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,6 @@
[![Commit activity](https://img.shields.io/github/commit-activity/m/GeoscienceAustralia/eo-tides)](https://img.shields.io/github/commit-activity/m/GeoscienceAustralia/eo-tides)
[![License](https://img.shields.io/github/license/GeoscienceAustralia/eo-tides)](https://img.shields.io/github/license/GeoscienceAustralia/eo-tides)

!!! warning

Note: This package is a work in progress, and not currently ready for operational use.

`eo-tides` provides provides powerful parallelized tools for integrating satellite Earth observation data with tide modelling. 🛠️🌊🛰️

`eo-tides` combines advanced tide modelling functionality from the [`pyTMD`](https://pytmd.readthedocs.io/en/latest/) package with [`pandas`](https://pandas.pydata.org/docs/index.html), [`xarray`](https://docs.xarray.dev/en/stable/) and [`odc-geo`](https://odc-geo.readthedocs.io/en/latest/), providing a suite of flexible tools for efficient analysis of coastal and ocean Earth observation data – from regional, continental, to global scale.
Expand Down
4 changes: 2 additions & 2 deletions eo_tides/eo.py
Original file line number Diff line number Diff line change
Expand Up @@ -209,7 +209,7 @@ def tag_tides(
added to the `xarray.DataArray` outputs. Defaults to "EOT20";
specify "all" to use all models available in `directory`.
For a full list of available and supported models, run
`eo_tides.model.list_models`.
`eo_tides.utils.list_models`.
directory : str, optional
The directory containing tide model data files. If no path is
provided, this will default to the environment variable
Expand Down Expand Up @@ -340,7 +340,7 @@ def pixel_tides(
added to the `xarray.DataArray` outputs. Defaults to "EOT20";
specify "all" to use all models available in `directory`.
For a full list of available and supported models, run
`eo_tides.model.list_models`.
`eo_tides.utils.list_models`.
directory : str, optional
The directory containing tide model data files. If no path is
provided, this will default to the environment variable
Expand Down
4 changes: 2 additions & 2 deletions eo_tides/model.py
Original file line number Diff line number Diff line change
Expand Up @@ -444,7 +444,7 @@ def model_tides(
The tide model (or list of models) to use to model tides.
Defaults to "EOT20"; specify "all" to use all models available
in `directory`. For a full list of available and supported models,
run `eo_tides.model.list_models`.
run `eo_tides.utils.list_models`.
directory : str, optional
The directory containing tide model data files. If no path is
provided, this will default to the environment variable
Expand Down Expand Up @@ -735,7 +735,7 @@ def model_phases(
The tide model (or list of models) to use to model tides.
Defaults to "EOT20"; specify "all" to use all models available
in `directory`. For a full list of available and supported models,
run `eo_tides.model.list_models`.
run `eo_tides.utils.list_models`.
directory : str, optional
The directory containing tide model data files. If no path is
provided, this will default to the environment variable
Expand Down
4 changes: 2 additions & 2 deletions eo_tides/stats.py
Original file line number Diff line number Diff line change
Expand Up @@ -246,7 +246,7 @@ def tide_stats(
returned as a `pandas.Dataframe`; otherwise a `pandas.Series`.
Defaults to "EOT20"; specify "all" to use all models available
in `directory`. For a full list of available and supported
models, run `eo_tides.model.list_models`.
models, run `eo_tides.utils.list_models`.
directory : str, optional
The directory containing tide model data files. If no path is
provided, this will default to the environment variable
Expand Down Expand Up @@ -453,7 +453,7 @@ def pixel_stats(
added to the `xarray.Dataset` output. Defaults to "EOT20";
specify "all" to use all models available in `directory`.
For a full list of available and supported models, run
`eo_tides.model.list_models`.
`eo_tides.utils.list_models`.
directory : str, optional
The directory containing tide model data files. If no path is
provided, this will default to the environment variable
Expand Down
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