Mostly use pixi and update data management

.gitattributes

@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true

.gitignore

@@ -50,3 +50,7 @@ site_*
 gapminder.arrow
 
 .ipynb_checkpoints/
+
+# pixi environments
+.pixi
+*.egg-info

.pre-commit-config.yaml

@@ -6,11 +6,11 @@ repos:
       # - id: check-hooks-apply  # Leave nbqa in here.
       # - id: identity  # Prints all files passed to pre-commits. Debugging.
   - repo: https://github.com/lyz-code/yamlfix
-    rev: 1.17.0
+    rev: 1.18.0
     hooks:
       - id: yamlfix
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: check-added-large-files
         args: [--maxkb=50000]
@@ -33,11 +33,11 @@ repos:
       - id: check-ast
       - id: check-docstring-first
   - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.35.1
+    rev: v1.37.1
     hooks:
       - id: yamllint
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.9
+    rev: v0.13.3
     hooks:
       # Run the linter.
       - id: ruff
@@ -48,14 +48,14 @@ repos:
       - id: ruff-format
         types_or: [python, pyi, jupyter]
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.7.1
+    rev: 0.8.1
     hooks:
       - id: nbstripout
         args:
           - --extra-keys
           - metadata.kernelspec metadata.language_info.version metadata.vscode
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.17
+    rev: 0.7.22
     hooks:
       - id: mdformat
         additional_dependencies: [mdformat-myst, mdformat-ruff]

plan.md

@@ -1,59 +1,84 @@
 1. Background
+
 1. Tools
+
    - Editors, comparison IDEs _(short)_
      - VS Code
      - Stata / Matlab / RStudio
      - In the end, VS Code encompasses most features of IDE + same for all languages
-   - Using LLMs effectively _\[long run\]_
-   - Using copilot effectively _\[long run\]_
+   - Using LLMs effectively _[long run]_
+   - Using copilot effectively _[long run]_
    - Communicating effectively (emails vs zoom vs in-person vs zulip) _(Video)_
    - Licenses _(Look up stuff)_
+
 1. Git and GitHub
+
 1. Python: Installation and Execution
+
    - Change to Pixi.
+
 1. Python basics
+
    - More on f-strings (could also do as an exercise)
-   - Reading object-oriented code _\[long run\]_
+   - Reading object-oriented code _[long run]_
+
 1. Intermediate Python
+
    - Decorators _(record anew, further material: Harrison)_
    - Custom data containers
    - Annotations
+
 1. Software engineering
+
    - Avoid nested if conditions _(record anew)_
    - formatting via pre-commit hooks _(record anew)_
-   - dags _\[long run\]_ - pytrees _\[long run\]_ - Don't be too smart
+   - dags _[long run]_ - pytrees _[long run]_ - Don't be too smart
      ([link](https://hackernoon.com/why-senior-devs-write-dumb-code-and-how-to-spot-a-junior-from-a-mile-away-27fa263b101a))
      _(set up examples, make scorecards / notebooks out of those, record short video)_
-   - When to code up something yourself and when to use a library _\[long run\], (record
+   - When to code up something yourself and when to use a library _[long run], (record
      screencast with recipes)_
+
 1. Reproducible research
+
    - Definition of "reproducible" - Pytask overview
    - Tiny Pytask example
    - Generating many tasks at once
    - Templates
+
 1. Data management with pandas
+
 1. Data Science
 
-- Machine learning with Scikit-learn
-- Econometrics with linearmodels
-- Econometrics with statsmodels
-
-12. Scientific computing
-
-- Numpy/scipy
-- Optimisation
-- Optimagic
-- Speedup
-
-13. Plotting
-01. Text data and texts
-
-- Encodings
-- Regexes _\[long run\]_
-- Simple Markdown
-- MystMD
-- Slidev
-- LaTeX
-- Detour: How to read a paper
-- Detour: How to structure a paper
-- Tables
+   - Machine learning with Scikit-learn
+   - Econometrics with linearmodels
+   - Econometrics with statsmodels
+
+1. Scientific computing
+
+   - Numpy/scipy
+   - Optimisation
+   - Optimagic
+   - Speedup
+
+1. Plotting
+
+1. Text data and texts
+
+   - Encodings
+   - Regexes _[long run]_
+   - Simple Markdown
+   - MystMD
+   - Slidev
+   - LaTeX
+   - Detour: How to read a paper
+   - Detour: How to structure a paper
+   - Tables
+
+1. Metrics / ML
+
+   - Overview
+   - Statsmodels: Intro
+   - Statsmodels: Results
+   - ML Intro
+   - scikit-learn: Intro
+   - scikit-learn: Hyperparameter tuning

pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "epp_topics"
 description = "Effective Programming Practices for Economists: Topics"
-requires-python = ">=3.11"
+requires-python = ">=3.13"
 dependencies = [
     "pytask"
 ]
@@ -51,6 +51,57 @@ source = "vcs"
 [tool.hatch.metadata]
 allow-direct-references = true
 
+
+[tool.pixi.workspace]
+channels = ["conda-forge"]
+platforms = ["linux-64"]
+
+[tool.pixi.dependencies]
+deepdiff = "*"
+gitpython = "*"
+ipykernel = "*"
+ipywidgets = "*"
+jupyter-book = "<2.0"
+jupyterlab = "*"
+line_profiler = "*"
+nlopt = "*"
+nodejs = "*"
+numba = "*"
+openpyxl = "*"
+optimagic = "*"
+pandas = ">=2.2"
+plotly = "*"
+pre-commit = "*"
+pyarrow = ">=19.0"
+pybaum = "*"
+pydata-sphinx-theme = ">=0.13.3"
+pygraphviz = "*"
+pytask = ">=0.5"
+pytest = "*"
+pytest-cov = "*"
+pytest-xdist = "*"
+python = "<3.14"
+pyyaml = "*"
+scikit-learn = "*"
+snakeviz = "*"
+sphinx = "*"
+sphinx-automodapi = "*"
+sphinx-copybutton = "*"
+sphinxcontrib-mermaid = "*"
+statsmodels = "*"
+toml = "*"
+xlrd = ">=1.0"
+
+
+[tool.pixi.pypi-dependencies]
+epp_topics = { path = ".", editable = true }
+fides = ">=0.7.4"
+jupytercards = "*"
+jupyterquiz = "*"
+kaleido = "*"
+pdbp = "*"
+pyperclip = "*"
+
 [tool.pytask.ini_options]
 paths = ["./src/epp_topics"]
 ignore = [
@@ -59,7 +110,7 @@ ignore = [
 ]
 
 [tool.ruff]
-target-version = "py311"
+target-version = "py313"
 fix = true
 line-length = 88
 
@@ -81,7 +132,6 @@ extend-ignore = [
     "N999", # Capitalized module name.
     "PD010",
     "PD015",
-    "PD901", # `df` used a lot as example variable name.
     "PERF401", # use a list comprehension.
     "PLR0913",
     "PLR2004",  # Magic value used in comparison.
@@ -95,10 +145,12 @@ extend-ignore = [
 ]
 
 [tool.ruff.lint.per-file-ignores]
-"src/epp_topics/python_basics/executing_pytest/screencast/example/test_cobb_douglas.py" = ["PLR2004"]
 "**/*.ipynb" = ["B018", "T201", "E402", "PLR2004"]
 "**/config.py" = ["N811"]
 "src/epp_topics/metrics_ml/**/objectives_materials.ipynb" = ["ERA001", "E501"]
+"src/epp_topics/python_basics/executing_pytest/screencast/example/test_cobb_douglas.py" = ["PLR2004"]
+"src/epp_topics/python_basics/pathlib/__init__.py" = ["A005"]
+"src/epp_topics/python_installation_execution_via_conda/config.py" = ["E501"]
 
 [tool.ruff.lint.pydocstyle]
 convention = "google"

src/epp_topics/_config.yml

@@ -10,7 +10,8 @@ description: >-
   Background on topics covering Python and reproducible research workflows
 # HTML-specific settings
 html:
-  google_analytics_id: G-JNV9WF0QCS
+  analytics:
+    google_analytics_id: G-JNV9WF0QCS
   home_page_in_navbar: false
   # Add GitHub buttons to your book
   # See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository
@@ -34,11 +35,11 @@ notebook_interface: notebook
 parse:
   myst_enable_extensions:
     - amsmath
-    - html_image
     - colon_fence
     - deflist
     - dollarmath
     - html_admonition
+    - html_image
     - linkify
     - smartquotes
 # Information about where the book exists on the web

src/epp_topics/background/file_systems/objectives_materials.ipynb

@@ -55,8 +55,7 @@
     "  `user_1`. On MacOS, `home` is called `Users` (with capital U).\n",
     "- `user_1` has personal documents and download directories.\n",
     "- `mambaforge` is a directory under `user_1` that contains the mamba package manager for\n",
-    "  creating Python environments (unless you choose to install the entire Anaconda Python\n",
-    "  distribution).\n",
+    "  creating Python environments.\n",
     "\n",
     "\n",
     "### Windows File System\n",

src/epp_topics/background/file_systems/screencast/slides.md

@@ -9,6 +9,7 @@ info: |
 drawings:
   persist: false
 transition: fade
+title: EPP — Background — File Systems
 defaults:
   layout: center
 ---

src/epp_topics/background/floats/screencast/slides.md

@@ -9,6 +9,7 @@ info: |
 drawings:
   persist: false
 transition: fade
+title: EPP — Background — Floating Point Numbers
 defaults:
   layout: center
 ---

src/epp_topics/background/graphs/screencast/slides.md

@@ -9,6 +9,7 @@ info: |
 drawings:
   persist: false
 transition: fade
+title: EPP — Background — A Primer on Graphs
 defaults:
   layout: center
 ---

src/epp_topics/background/os_history/screencast/slides.md

@@ -9,6 +9,7 @@ info: |
 drawings:
   persist: false
 transition: fade
+title: EPP — Background — A Brief History of Operating Systems
 defaults:
   layout: center
 ---

src/epp_topics/chapter_template/subchapter_1/screencast/slides.md

@@ -9,6 +9,7 @@ info: |
 drawings:
   persist: false
 transition: fade
+title: EPP — Template — Subchapter Title
 defaults:
   layout: center
 ---

src/epp_topics/config.py

@@ -15,6 +15,7 @@
     "tools",
     "git",
     "python_installation_execution",
+    "python_installation_execution_via_conda",
     "python_basics",
     "debugging",
     "software_engineering",