Add estimagic logo to documentation page (#467)

.gitignore

@@ -74,6 +74,8 @@ docs/_build/
 docs/build/
 docs/source/_build/
 docs/source/getting_started/*.db
+docs/source/getting_started/*.db-shm
+docs/source/getting_started/*.db-wal
 docs/source/refs.bib.bak
 
 # PyBuilder

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ repos:
       - id: check-useless-excludes
         # - id: identity  # Prints all files passed to pre-commits. Debugging.
   - repo: https://github.com/lyz-code/yamlfix
-    rev: 1.10.0
+    rev: 1.13.0
     hooks:
       - id: yamlfix
         exclude: tests/optimization/fixtures
@@ -57,17 +57,17 @@ repos:
       - id: yamllint
         exclude: tests/optimization/fixtures
   - repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 23.7.0
     hooks:
       - id: black
         language_version: python3.10
   - repo: https://github.com/asottile/blacken-docs
-    rev: 1.13.0
+    rev: 1.15.0
     hooks:
       - id: blacken-docs
         exclude: docs/source/how_to_guides/optimization/how_to_specify_constraints.md
   - repo: https://github.com/PyCQA/docformatter
-    rev: v1.7.1
+    rev: v1.7.5
     hooks:
       - id: docformatter
         args:
@@ -78,8 +78,8 @@ repos:
           - '88'
           - --blank
         exclude: src/estimagic/optimization/algo_options.py
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.270
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.282
     hooks:
       - id: ruff
   - repo: https://github.com/nbQA-dev/nbQA
@@ -110,7 +110,7 @@ repos:
           - '88'
         files: (docs/.)
   - repo: https://github.com/asottile/setup-cfg-fmt
-    rev: v2.3.0
+    rev: v2.4.0
     hooks:
       - id: setup-cfg-fmt
   - repo: https://github.com/mgedmin/check-manifest

codecov.yml

@@ -9,7 +9,7 @@ coverage:
   status:
     patch:
       default:
-        target: 70%
+        target: 30%
     project:
       default:
         target: 90%
@@ -25,3 +25,4 @@ ignore:
   - src/estimagic/optimization/subsolvers/_steihaug_toint_fast.py
   - src/estimagic/optimization/subsolvers/gqtpar_fast.py
   - src/estimagic/optimization/tranquilo/clustering.py
+  - tests/optimization/test_tao_optimizers.py

docs/rtd_environment.yml

@@ -16,7 +16,7 @@ dependencies:
   - ipython
   - ipython_genutils
   - myst-nb
-  - pydata-sphinx-theme<=0.12.0
+  - pydata-sphinx-theme
   - pybaum
   - matplotlib
   - seaborn

docs/source/conf.py

@@ -77,7 +77,6 @@
     "petsc4py",
     "statsmodels",
     "numba",
-    "tranquilo",
 ]
 
 extlinks = {
@@ -163,7 +162,7 @@
 # a list of builtin themes.
 html_theme = "pydata_sphinx_theme"
 
-html_logo = "_static/images/logo.svg"
+html_logo = "_static/images/estimagic_logo.svg"
 
 html_theme_options = {
     "github_url": "https://github.com/OpenSourceEconomics/estimagic",

docs/source/index.md

@@ -1,4 +1,11 @@
-# estimagic
+```{raw} html
+<div id="logo" style="text-align:center;">
+<img src="_static/images/estimagic_logo.svg" alt="estimagic icon" height="100" />
+</div>
+```
+
+<br>
+<br>
 
 estimagic is a Python package for nonlinear optimization with or without constraints. It
 is particularly suited to solve difficult nonlinear estimation problems. On top, it

pyproject.toml

@@ -85,7 +85,6 @@ filterwarnings = [
     "ignore:In a future version, the Index constructor will not infer numeric dtypes when passed object-dtype sequences",
     "ignore:distutils Version classes are deprecated. Use packaging.version instead",
     "ignore:Standard matrix inversion failed due to LinAlgError",
-    "ignore:Tranquilo is extremely experimental",
     "ignore:delta_grad == 0.0",
     "ignore:Widget._active_widgets is deprecated",
     "ignore:Widget._widget_types is deprecated",

src/estimagic/optimization/tranquilo.py

@@ -6,7 +6,7 @@
     from functools import partial
     from estimagic.decorators import mark_minimizer
 
-    tranquilo = mark_minimizer(
+    tranquilo_scalar = mark_minimizer(
         func=partial(_tranquilo, functype="scalar"),
         name="tranquilo",
         primary_criterion_entry="value",
@@ -24,6 +24,6 @@
         is_global=False,
     )
 
-    __all__ = ["tranquilo", "tranquilo_ls"]
+    __all__ = ["tranquilo_scalar", "tranquilo_ls"]
 else:
     __all__ = []

src/estimagic/parameters/parameter_groups.py

@@ -38,7 +38,6 @@ def get_params_groups_and_short_names(params, free_mask, max_group_size=8):
     if len(pd.unique(groups)) == len(groups):
         groups = ["Parameters"] * len(groups)
 
-    groups = groups
     counts = pd.value_counts(groups)
     to_be_split = counts[counts > max_group_size]
     for group_name, n_occurrences in to_be_split.items():

tests/optimization/test_tao_optimizers.py

@@ -78,7 +78,7 @@ def test_max_iters():
         algo_options={"stopping.max_iterations": 25},
     )
 
-    assert result.message == "user defined" or result.message == "step size small"
+    assert result.message in ("user defined", "step size small")
 
 
 def test_grtol():
@@ -99,9 +99,9 @@ def test_grtol():
         },
     )
 
-    assert (
-        result.message == "relative_gradient_tolerance below critical value"
-        or result.message == "step size small"
+    assert result.message in (
+        "relative_gradient_tolerance below critical value",
+        "step size small",
     )
 
 
@@ -123,9 +123,9 @@ def test_gatol():
         },
     )
 
-    assert (
-        result.message == "absolute_gradient_tolerance below critical value"
-        or result.message == "step size small"
+    assert result.message in (
+        "absolute_gradient_tolerance below critical value",
+        "step size small",
     )
 
 
@@ -147,9 +147,9 @@ def test_gttol():
         },
     )
 
-    assert (
-        result.message == "gradient_total_tolerance below critical value"
-        or result.message == "step size small"
+    assert result.message in (
+        "gradient_total_tolerance below critical value",
+        "step size small",
     )