Merge pull request #17 from scientificcomputing/final-fixes

Final fixes
scientificcomputing · Nov 22, 2023 · 46a3dca · 46a3dca
2 parents e6e23af + 075cf03
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diff --git a/docs/intro.md b/docs/intro.md
@@ -26,24 +26,29 @@ Henrik Finsberg, Jørgen Dokken and Min Ragan-Kelley
 * We write code to **run simulations**
 * We write code to create figures and tables (**post-processing**)
 
-* Whenever you publish a paper, you need to have recipe for how to reproduce the results in the paper
-    - Many journals require that you make your code available
+
+---
+
+
+*Whenever you publish a paper, you need to have recipe for how to reproduce the results in the paper*
+
+* Many journals require that you make your code available
 
 ---
 
 ## Goal of this workshops
 
-- 11.15 - 11.45: Code and data repositories (Henrik)
-- 11.45 - 12.15: Reproducible environments (Min)
-- 12.15 - 12.45: Lunch
-- 12.45 - 13.15: Linters, formatters and continuous integration (Henrik + Jørgen)
-- 13.15 - 13.45: Documentation (Jørgen)
-- 13.45 - 14.00: Break
-- 14.00 - 14.30: A paper with code (Henrik)
+- 11.00 - 11.30: Code and data repositories (Henrik)
+- 11.30 - 12.00: Reproducible environments (Min)
+- 12.00 - 12.30: Lunch
+- 12.30 - 13.00: Linters, formatters and continuous integration (Henrik + Jørgen)
+- 13.00 - 13.30: Documentation (Jørgen)
+- 13.30 - 13.45: Break
+- 13.45 - 14.15: A paper with code (Henrik)
 
 ---
 
 ## Material from the workshop
 
 - https://github.com/scientificcomputing/seminar-23-11-2023
-- https://scientificcomputing.github.io/seminar-23-11-2023/README.html
+- https://scientificcomputing.github.io/seminar-23-11-2023
diff --git a/docs/paper.md b/docs/paper.md
@@ -110,7 +110,11 @@ Several ways to do this:
 * Ideally you should share the data on Zenodo (https://zenodo.org) when publishing the paper. This will make sure you get a DOI for the data.
   - It is also possible to upload data with restricted data on Zenodo
 * Create a script for downloading data
+  - https://github.com/scientificcomputing/example-paper-fenics
+  - Dropbox: Use `?dl=1`
+  - Google drive: `https://drive.google.com/uc?export=download&id=DRIVE_FILE_ID`
 
+---
 
 ## Make sure to create a tag / release
 
@@ -134,3 +138,11 @@ You should create a tag (and a release) of the code
 
 - Citation information
   - Write a `CITATION.cff`
+
+
+---
+
+## Next steps
+
+- Check out the material at https://github.com/scientificcomputing/seminar-23-11-2023
+- Ask us for help - email, slack or in the office
diff --git a/docs/repo.md b/docs/repo.md
@@ -32,16 +32,16 @@ Henrik Finsberg
 
 ## Setting up your first project
 
-- Cookiecutters
-    - Script that generate the files based on a few questions
-    - https://github.com/scientificcomputing/generate-paper
-    - https://github.com/scientific-python/cookie
-    - https://www.cookiecutter.io/templates
 - Templates
     - Copy all files from an existing repository
     - https://github.com/scientificcomputing/example-paper
     - https://github.com/scientificcomputing/example-paper-fenics
 
+- Cookiecutters
+    - Script that generate the files based on a few questions
+    - https://github.com/scientificcomputing/generate-paper
+    - https://github.com/scientific-python/cookie
+    - https://www.cookiecutter.io/templates
 
 ---
 
@@ -90,12 +90,6 @@ research_paper_1
 
 ---
 
-![bg w:50%](https://the-turing-way.netlify.app/_images/healthy-research-tree.jpg)
-<style scoped>section { justify-content: end; }</style>
-<p class="small-text">Image is used under a CC-BY 4.0 licence. DOI: 10.5281/zenodo.3332807.</p>
-
----
-
 ## Code review process
 
 * Open issue describing the problem. Use the issue tracker to discuss whether this needs to be solved.
@@ -112,13 +106,7 @@ If you work alone and don't work on multiple things at the same time, the it is
 
 ---
 
-# Demo
-
-- Create a new branch and open a pull request
-
----
-
-# Exercise
+# Demo / Exercise
 
 - Create a new repo on GitHub (ex: `example-paper`)
 - Run the cookiecutter and add all the files in a single commit
@@ -152,7 +140,8 @@ If you work alone and don't work on multiple things at the same time, the it is
 ## Versioning
 
 * When you think that your code is ready for external users, it is time to create your first release
-* Your code should get a version number
+* Your code should get a version number.
+* Create a release when you submit your paper.
 * `MAJOR.MINOR.MICRO`
 * Specify the version number in `pyproject.toml`
 * Semantic or Calendar based versioning
@@ -177,7 +166,7 @@ https://calver.org
 https://semver.org
 
 - `major.minor.micro` e.g `0.1.2`
-- Bump patch: Bug fixes not affecting the API
+- Bump micro / patch: Bug fixes not affecting the API
 - Bump minor: Backward compatible API additions/changes
 - Bump major: Backward incompatible API changes
 - Typically start with `0` major version and bump to `1` when ready for users.
@@ -216,11 +205,7 @@ https://semver.org
 
 ---
 
-Demo: Creating a new release
-
----
-
-## Exercise: bump the version
+## Demo / Exercise: bump the version
 
 - Change the version of your paper
 - Create a new tag and release
@@ -248,14 +233,32 @@ https://choosealicense.com
 
 ## Exercise:
 
-You would like to implement a new feature in dolfinx:
+You want to use dolfinx:
+https://github.com/FEniCS/dolfinx
+
+What license do you need to use?
+
+---
+
+You can choose if you want to use GPL or LGPL.
+- If you choose GPL, you need to use GPL license
+- If you choose LGPL, you can choose another license
+
+---
+
+## Exercise:
+
+You would like to implement a new feature in dolfinx and use it in your code:
 https://github.com/FEniCS/dolfinx
 
 What license do you need to use?
+* GPL or LGPL
 
 ---
 
 
+
+
 Are you allowed to copy code from a repo with MIT license into your own repo?
 
 ```

diff --git a/docs/testing.md b/docs/testing.md
@@ -2,7 +2,7 @@
 theme: default
 paginate: true
 header: 'Best Practices in Modern Software Development: Linters, formatters and pre-commit hooks'
-footer: '23.11.23 - Henrik Finsberg and Jørgen Dokken'
+footer: '23.11.23 - Henrik Finsberg'
 size: 16:9
 style: |
   .small-text {
@@ -15,7 +15,7 @@ marp: true
 # Linters, formatters and pre-commit hooks
 Best Practices in Modern Software Development: 23.11.23
 
-Henrik Finsberg and Jørgen Dokken
+Henrik Finsberg
 
 ---
 
@@ -31,7 +31,7 @@ Henrik Finsberg and Jørgen Dokken
 - [`flake8`](https://github.com/PyCQA/flake8): points out general problems
 - [`ruff`](https://github.com/astral-sh/ruff): similar to `flake8` only more and faster (recommended). `ruff` also include features from `isort`, `pyupgrade`, `black`, ...
 
-* You can install them with `pip` or `pipx` [FIXME: Talk about `pipx`?]
+* You can install them with `pip` or `pipx`
 
 ---