Tutorial 2 - scientific Python ecosystem: pandas and GeoPandas: Add JN #4

yvonnefroehlich · 2024-09-22T17:29:29Z

This PR adds the Jupyter notebook for Tutorial 2 - scientific Python ecosystem: pandas and GeoPandas:

Data stored as pandas DataFrame and GeoPandas GeoDataFrame
Different geometries (point, lines, polygons)
Choropleth map
Handling aspatial data
Filtering and using different styles / files for plotting
Conversion of objects from other python packages to geopandas related objects

Preview:

weiji14

Notebook looks very clean and easy to follow so far! Just some minor suggestions for now, not sure if you're planning to add more materials to this notebook?

book/tut2_spec_pd_gpd.ipynb

yvonnefroehlich · 2024-11-13T17:14:59Z

Notebook looks very clean and easy to follow so far! Just some minor suggestions for now, not sure if you're planning to add more materials to this notebook?

Thanks @weiji14 for already looking at this JN and the positive feedback! I feel the general structure should be finished. What is missing is some documentation and improvements of the formulations, as you already suggested.

Co-authored-by: Wei Ji <[email protected]>

yvonnefroehlich · 2024-11-17T01:05:18Z

Just a simple suggestion, using individual cells can help beginners understand how to set a region. For example, they can observe the data range beforehand through print(df_jp_eqs["magnitude"].min(), df_jp_eqs["magnitude"].max()) to demonstrates how to visualize data limits.

This is a good suggestions! Moved these lines to a separate cell.

book/tut2_spec_pd_gpd.ipynb

Esteban82 · 2024-11-22T13:21:28Z

I think is ready to merge. My only minor suggestion would be to add a frame to the choropleth map.

book/tut2_spec_pd_gpd.ipynb

yvonnefroehlich · 2024-11-23T18:31:04Z

book/_toc.yml

@@ -13,3 +13,4 @@ parts:
  - file: markdown
  - file: notebooks
  - file: markdown-notebooks
+  - file: tut2_spec_pd_gpd


Maybe it's better to add the file names of the JNs or files together within one PR to avoid merge conflicts.

Let's just leave it as is, it'll be a good example to learn how to handle merge conflicts 🙂

Ok, first tutorial is merged, so you'll need to resolve the merge conflict here. If you could also rename the file to tut02_spec_pd_gpd (add an extra 0), that would make it consistent with the first tutorial.

yvonnefroehlich · 2024-11-23T18:32:48Z

environment.yml

+  # Tutorial 2 - pandas and GeoPandas, Tutorial 4 - Geophysics (Seismology)
+  - pandas=2.2.2
+  - geopandas=1.0.1


Same as above, maybe better to update the environment.yml within one PR for all tutorials to avoid merge conflicts.

Since pandas is a required dependency of pygmt, this won't need to be added here, unless you specifically require pandas=2.2.2?

Note that I'll be updating the conda-lock.yml file to pin all dependencies once all the tutorial notebooks are merged, so that people can reproduce the exact dependency versions in the future (including pandas).

I don't think I specifically need this pandas version. Just added the version I am currently having installed in the virtual environment I am using for this pre-workshop.

Ok, we can leave the pin on pandas=2.2.2, sometimes good to be explicit.

weiji14

This tutorial is next in line to be merged! @yvonnefroehlich, if you can handle the merge conflict on _toc.yml, and maybe add some commentary around fig.legend, I can merge this in the next 24hours.

book/tut2_spec_pd_gpd.ipynb

weiji14 · 2024-11-27T20:41:50Z

book/tut2_spec_pd_gpd.ipynb

+    "# Add a heading (+H) to the legend and adjust the font size (+f) to 9 points\n",
+    "fig.plot(data=gpd_rivers_short, pen=\"0.5p,orange\", label=f\"shorter {len_limit} m+Hriver length+f9p\")\n",
+    "fig.plot(data=gpd_rivers_long, pen=\"0.5p,darkred\", label=f\"longer {len_limit} m\")\n",
+    "\n",
+    "fig.legend(position=\"jLT+o0.1c\", box=\"+gwhite@30+p0.1p,gray50\")\n",


Since fig.legend isn't explained in the first tutorial, could you add some text to explain it before the code cell? You can just link to https://www.pygmt.org/v0.13.0/api/generated/pygmt.Figure.legend.html and/or one of the PyGMT gallery examples using legend.

Makes sense! I have added some documentation in commit 909f713.

weiji14 · 2024-11-27T20:43:05Z

environment.yml

+  # Tutorial 2 - pandas and GeoPandas, Tutorial 4 - Geophysics (Seismology)
+  - pandas=2.2.2
+  - geopandas=1.0.1


Ok, we can leave the pin on pandas=2.2.2, sometimes good to be explicit.

Co-authored-by: Wei Ji <[email protected]>

yvonnefroehlich · 2024-11-28T09:08:06Z

This tutorial is next in line to be merged! @yvonnefroehlich, if you can handle the merge conflict on _toc.yml, and maybe add some commentary around fig.legend, I can merge this in the next 24hours.

Sounds good! Have resolved the merge conflict and added the leading "0" to the file name (b7f789e).

weiji14 · 2024-11-28T09:28:52Z

Thanks again @yvonnefroehlich, this PR is merged and tutorial is now up at https://www.generic-mapping-tools.org/agu24workshop/tut02_spe_pd_gpd.html 🎉. Feel free to open a PR for any minor changes (if needed) before the workshop.

yvonnefroehlich · 2024-11-28T11:44:19Z

book/_toc.yml

@@ -14,3 +14,4 @@ parts:
  - file: notebooks
  - file: markdown-notebooks
  - file: tut01_firstfigure
+  - file: tut02_spec_pd_gpd


Maybe we should use "spe" instead of "spec" as the later one seems to refere to scientific Python ecosystem coordination (please see https://scientific-python.org/specs/ [, and Dongdong's very detailed review on my draft for the pygmt talk])?

yvonnefroehlich added 2 commits September 22, 2024 19:20

Add set up of JN for pandas geopandas tutorial

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Remove checkpoints

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yvonnefroehlich added the enhancement New feature or request label Sep 22, 2024

yvonnefroehlich self-assigned this Sep 22, 2024

Fix typos

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yvonnefroehlich marked this pull request as draft September 22, 2024 18:12

yvonnefroehlich and others added 4 commits September 23, 2024 09:56

Merge branch 'main' into add-jn-pd-gpd

a493ebe

Add geopandas polygon example, Update all examples, Add documentation

e98c4ea

Add to tutorial list in _toc.yml

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Merge remote-tracking branch 'origin/main' into add-jn-pd-gpd

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yvonnefroehlich changed the title ~~WIP: Add JN for tutorial on pandas and geopandas~~ WIP: Add JN for tutorial 3 on pandas and geopandas Nov 9, 2024

yvonnefroehlich changed the title ~~WIP: Add JN for tutorial 3 on pandas and geopandas~~ WIP: Add JN for tutorial 3 on pandas and GeoPandas Nov 9, 2024

yvonnefroehlich changed the title ~~WIP: Add JN for tutorial 3 on pandas and GeoPandas~~ WIP: Add JN for tutorial 2 on pandas and GeoPandas Nov 9, 2024

Make file name for descriptive | Update intro cell

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yvonnefroehlich mentioned this pull request Nov 9, 2024

Make review of Jupyter notebooks more convenient #9

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Remove old file

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yvonnefroehlich changed the title ~~WIP: Add JN for tutorial 2 on pandas and GeoPandas~~ WIP: Tutorial 2 - SPEC: pandas and GeoPandas: Add JN Nov 9, 2024

yvonnefroehlich changed the title ~~WIP: Tutorial 2 - SPEC: pandas and GeoPandas: Add JN~~ WIP: Tutorial 2 - scientific Python ecosystem: pandas and GeoPandas: Add JN Nov 9, 2024

yvonnefroehlich added 4 commits November 9, 2024 21:38

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weiji14 reviewed Nov 13, 2024

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yvonnefroehlich and others added 4 commits November 13, 2024 18:19

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Co-authored-by: Wei Ji <[email protected]>

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Co-authored-by: Wei Ji <[email protected]>

Add docs | Fix typos | Fix and add links

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yvonnefroehlich changed the title ~~WIP: Tutorial 2 - scientific Python ecosystem: pandas and GeoPandas: Add JN~~ Tutorial 2 - scientific Python ecosystem: pandas and GeoPandas: Add JN Nov 13, 2024

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yvonnefroehlich added 2 commits November 23, 2024 14:04

Expand docs

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Add needed packages and versions to 'enviorment.yml'

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yvonnefroehlich added 5 commits November 24, 2024 01:18

Add comment regarding OGR formats

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Introduce variable 'dpi_imag' for resolution of images within JN

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yvonnefroehlich and others added 5 commits November 28, 2024 09:18

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Co-authored-by: Wei Ji <[email protected]>

Merge branch 'main' into add-jn-pd-gpd

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Rename JN - add leading 0

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weiji14 merged commit 99dde5d into main Nov 28, 2024
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Tutorial 2: Fix typos #18

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Tutorial 2 - scientific Python ecosystem: pandas and GeoPandas: Add JN #4

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