Styling (#13)

* Fix docs * Fix docs * Fix docs --------- Co-authored-by: Thomas Pinder <pinthoma@amazon.com>
amazon-science · Sep 9, 2024 · 7507996 · 7507996
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diff --git a/docs/examples/azcausal.ipynb b/docs/examples/azcausal.ipynb
@@ -53,7 +53,7 @@
     "\n",
     "linear_trend = Trend(degree=1, coefficient=0.05)\n",
     "data = linear_trend(simulate(cfg))\n",
-    "plot(data)"
+    "ax = plot(data)"
    ]
   },
   {
@@ -76,7 +76,7 @@
     "TRUE_EFFECT = 0.05\n",
     "effect = StaticEffect(effect=TRUE_EFFECT)\n",
     "inflated_data = effect(data)\n",
-    "plot(inflated_data)"
+    "ax = plot(inflated_data)"
    ]
   },
   {
@@ -121,14 +121,18 @@
     "in effort to fully stress-test any new model and identify its limitations.\n",
     "\n",
     "To achieve this, we'll simulate 10 control units, 60 pre-intervention time points, and\n",
-    "30 post-intervention time points according to the following process: $$ \\begin{align}\n",
+    "30 post-intervention time points according to the following process: \n",
+    "\n",
+    "$$ \\begin{align}\n",
     "\\mu_{n, t} & \\sim\\mathcal{N}(20, 0.5^2)\\\\\n",
     "\\alpha_{n} & \\sim \\mathcal{N}(0, 1^2)\\\\\n",
     "\\beta_{n} & \\sim \\mathcal{N}(0.05, 0.01^2)\\\\\n",
     "\\nu_n & \\sim \\mathcal{N}(1, 1^2)\\\\\n",
     "\\gamma_n & \\sim \\operatorname{Student-t}_{10}(1, 1^2)\\\\\n",
     "\\mathbf{Y}_{n, t} & = \\mu_{n, t} + \\alpha_{n} + \\beta_{n}t + \\nu_n\\sin\\left(3\\times\n",
-    "2\\pi t + \\gamma\\right) + \\delta_{t, n} \\end{align} $$ where the true treatment effect\n",
+    "2\\pi t + \\gamma\\right) + \\delta_{t, n} \\end{align} $$ \n",
+    "\n",
+    "where the true treatment effect\n",
     "$\\delta_{t, n}$ is 5% when $n=1$ and $t\\geq 60$ and 0 otherwise. Meanwhile,\n",
     "$\\mathbf{Y}$ is the matrix of observations, long in the number of time points and wide\n",
     "in the number of units."
@@ -159,7 +163,7 @@
     "periodic = Periodic(amplitude=amplitude, shift=shift, frequency=3)\n",
     "\n",
     "data = effect(periodic(linear_trend(simulate(cfg))))\n",
-    "plot(data)"
+    "ax = plot(data)"
    ]
   },
   {
@@ -193,6 +197,9 @@
    "cell_metadata_filter": "title,-all",
    "main_language": "python",
    "notebook_metadata_filter": "-all"
+  },
+  "language_info": {
+   "name": "python"
   }
  },
  "nbformat": 4,

diff --git a/docs/examples/basic.ipynb b/docs/examples/basic.ipynb
@@ -77,7 +77,7 @@
     ")\n",
     "\n",
     "data = simulate(cfg)\n",
-    "plot(data)"
+    "ax = plot(data)"
    ]
   },
   {
@@ -113,7 +113,7 @@
     "        global_scale=s,\n",
     "    )\n",
     "    data = simulate(cfg)\n",
-    "    plot(data, ax=ax, title=f\"Mean: {m}, Scale: {s}\")"
+    "    _ = plot(data, ax=ax, title=f\"Mean: {m}, Scale: {s}\")"
    ]
   },
   {
@@ -162,7 +162,7 @@
     "fig, axes = plt.subplots(ncols=2, figsize=(10, 3))\n",
     "for ax in axes:\n",
     "    data = simulate(cfg)\n",
-    "    plot(data, ax=ax)"
+    "    _ = plot(data, ax=ax)"
    ]
   },
   {
@@ -180,13 +180,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "\n",
     "rng = np.random.RandomState(42)\n",
     "\n",
     "fig, axes = plt.subplots(ncols=2, figsize=(10, 3))\n",
     "for ax in axes:\n",
     "    data = simulate(cfg, key=rng)\n",
-    "    plot(data, ax=ax)"
+    "    _ = plot(data, ax=ax)"
    ]
   },
   {
@@ -213,8 +212,8 @@
     "effect = StaticEffect(effect=0.02)\n",
     "inflated_data = effect(data)\n",
     "fig, (ax0, ax1) = plt.subplots(ncols=2, figsize=(10, 3))\n",
-    "plot(data, ax=ax0, title=\"Original data\")\n",
-    "plot(inflated_data, ax=ax1, title=\"Inflated data\")"
+    "ax0 = plot(data, ax=ax0, title=\"Original data\")\n",
+    "ax1 = plot(inflated_data, ax=ax1, title=\"Inflated data\")"
    ]
   },
   {
@@ -238,7 +237,7 @@
    "source": [
     "trend_term = Trend(degree=1, coefficient=0.1)\n",
     "data_with_trend = effect(trend_term(data))\n",
-    "plot(data_with_trend)"
+    "ax = plot(data_with_trend)"
    ]
   },
   {
@@ -250,7 +249,7 @@
    "source": [
     "trend_term = Trend(degree=2, coefficient=0.0025)\n",
     "data_with_trend = effect(trend_term(data))\n",
-    "plot(data_with_trend)"
+    "ax = plot(data_with_trend)"
    ]
   },
   {
@@ -270,7 +269,7 @@
    "source": [
     "periodicity = Periodic(amplitude=2, frequency=6)\n",
     "perioidic_data = effect(periodicity(trend_term(data)))\n",
-    "plot(perioidic_data)"
+    "ax = plot(perioidic_data)"
    ]
   },
   {
@@ -292,7 +291,7 @@
     "intercept = UnitVaryingParameter(sampling_dist=sampling_dist)\n",
     "trend_term = Trend(degree=1, intercept=intercept, coefficient=0.1)\n",
     "data_with_trend = effect(trend_term(data))\n",
-    "plot(data_with_trend)"
+    "ax = plot(data_with_trend)"
    ]
   },
   {
@@ -306,7 +305,7 @@
     "frequency = UnitVaryingParameter(sampling_dist=sampling_dist)\n",
     "\n",
     "p = Periodic(frequency=frequency)\n",
-    "plot(p(data))"
+    "ax = plot(p(data))"
    ]
   },
   {
@@ -322,7 +321,7 @@
     "variation. In a follow-up notebook, we show how these datasets may be integrated with\n",
     "Amazon's own AZCausal library to compare the effect estimated by a model with the true\n",
     "effect of the underlying data generating process. A link to this notebook is\n",
-    "[here](https://github.com/amazon-science/causal-validation/blob/main/examples/azcausal.pct.py)."
+    "[here](http://localhost:9998/causal-validation/examples/azcausal/)."
    ]
   }
  ],
@@ -331,6 +330,9 @@
    "cell_metadata_filter": "title,-all",
    "main_language": "python",
    "notebook_metadata_filter": "-all"
+  },
+  "language_info": {
+   "name": "python"
   }
  },
  "nbformat": 4,

diff --git a/docs/examples/placebo_test.ipynb b/docs/examples/placebo_test.ipynb
@@ -73,7 +73,7 @@
     "TRUE_EFFECT = 0.05\n",
     "effect = StaticEffect(effect=TRUE_EFFECT)\n",
     "data = effect(simulate(cfg))\n",
-    "plot(data)"
+    "ax = plot(data)"
    ]
   },
   {

diff --git a/docs/installation.md b/docs/installation.md
@@ -4,39 +4,39 @@
 
 The latest stable release of `causal-validation` can be installed via `pip`:
 
-```bash
+``` bash
 pip install causal-validation
 ```
 
-!!! note "Check your installation"
-    We recommend you check your installation version:
-    ```
-    python -c 'import causal_validation; print(causal_validation.__version__)'
-    ```
+We recommend you check your installation version:
+
+``` bash
+python -c 'import causal_validation; print(causal_validation.__version__)'
+```
 
 ## Development version
 
 !!! warning
     This version is possibly unstable and may contain bugs.
 
-    The latest development version of `causal_validation` can be installed via running following:
 
-    ```bash
-    git clone git@github.com:amazon-science/causal-validation.git
-    cd causal-validation
-    hatch shell create
-    ```
+The latest development version of `causal_validation` can be installed via running following:
 
-!!! tip
-    We advise you create virtual environment before installing:
+``` bash
+git clone git@github.com:amazon-science/causal-validation.git;
+cd causal-validation;
+hatch shell create
+```
 
-    ```bash
-    conda create -n causal-validation python=3.11.0
-    conda activate causal-validation
-    ```
+We advise you create virtual environment before installing:
+
+``` bash
+conda create -n causal-validation python=3.11.0;
+conda activate causal-validation
+```
 
-    and recommend you check your installation passes the supplied unit tests:
+and recommend you check your installation passes the supplied unit tests:
 
-    ```bash
-    hatch run dev:test
-    ```
+``` bash
+hatch run dev:test
+```
diff --git a/docs/javascripts/mathjax.js b/docs/javascripts/mathjax.js
@@ -0,0 +1,19 @@
+window.MathJax = {
+  tex: {
+    inlineMath: [["\\(", "\\)"]],
+    displayMath: [["\\[", "\\]"]],
+    processEscapes: true,
+    processEnvironments: true
+  },
+  options: {
+    ignoreHtmlClass: ".*|",
+    processHtmlClass: "arithmatex"
+  }
+};
+
+document$.subscribe(() => {
+  MathJax.startup.output.clearCache()
+  MathJax.typesetClear()
+  MathJax.texReset()
+  MathJax.typesetPromise()
+})
diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css
@@ -0,0 +1,9 @@
+[data-md-color-scheme="reds"] {
+    --md-primary-fg-color:        #b5121b;
+    --md-primary-fg-color--light: #ECB7B7;
+    --md-primary-fg-color--dark:  #7d030b;
+}
+
+/* :root > * { */
+  /* --md-code-bg-color: #0FF1CE; */
+/* } */
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -20,10 +20,23 @@ theme:
     - navigation.sections
     - search.suggest
     - content.code.copy
+  palette:
+    scheme: reds
 
 markdown_extensions:
   - abbr
   - admonition
+  - pymdownx.superfences
+  - pymdownx.inlinehilite
+  - pymdownx.arithmatex:
+      generic: true
+  - pymdownx.highlight:
+      anchor_linenums: true
+      line_spans: __span
+      use_pygments: true
+      pygments_lang_class: true
+      pygments_style: autumn
+      noclasses: true
 
 plugins:
   - search
@@ -35,5 +48,12 @@ extra:
   version:
     provider: mike
 
+extra_css:
+  - stylesheets/extra.css
+
+extra_javascript:
+  - javascripts/mathjax.js
+  - https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js
+
 watch:
   - src
diff --git a/src/causal_validation/__about__.py b/src/causal_validation/__about__.py
@@ -1,3 +1,3 @@
-__version__ = "0.0.5"
+__version__ = "0.0.6"
 
 __all__ = ["__version__"]