Merge pull request #100 from zfit/docs/fixes_intersphinx

docs: fix typo, add gitignore, remove obsolet MANIFEST.in
zfit · Nov 12, 2024 · 2ef7228 · 2ef7228
2 parents b0839e2 + b335249
commit 2ef7228
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diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -7,20 +7,15 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.9"
+    python: "mambaforge-22.9"
 
 
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
 
-formats: [ ]
+conda:
+  environment: docs/environment.yml
 
-python:
-  install:
-    - requirements: docs/additional_requirements.txt
-    - method: pip
-      path: .
-      extra_requirements:
-        - dev
+formats: [ ]
diff --git a/docs/.gitignore b/docs/.gitignore
@@ -0,0 +1,2 @@
+/_build/
+/api/*.rst
diff --git a/docs/api/static/zfit_physics.compwa.rst b/docs/api/static/zfit_physics.compwa.rst
@@ -9,7 +9,7 @@ Import the module with:
 
     import zfit_physics.compwa as zcompwa
 
-This will enable that :py:function:`~ tensorwaves.estimator.Estimator`, can be used as a loss function in zfit minimizers as
+This will enable that a :py:class:`~ tensorwaves.estimator.Estimator`, for example ``estimator`` in the following, can be used as a loss function in zfit minimizers as
 
 .. code-block:: python
 

diff --git a/docs/api/static/zfit_physics.roofit.rst b/docs/api/static/zfit_physics.roofit.rst
@@ -11,26 +11,53 @@ For example via conda:
 
     $ mamba install -c conda-forge root
 
+.. jupyter-execute::
+    :hide-code:
+    :hide-output:
+
+    import numpy as np
+    import zfit
+    from ROOT import RooArgSet, RooDataSet, RooGaussian, RooRealVar
+
+    data = np.random.normal(loc=2.0, scale=3.0, size=1000)
+
+    mur = RooRealVar("mu", "mu", 1.2, -4, 6)
+    sigmar = RooRealVar("sigma", "sigma", 1.3, 0.5, 10)
+    obsr = RooRealVar("x", "x", -2, 3)
+    RooFit_gauss = RooGaussian("gauss", "gauss", obsr, mur, sigmar)
+
+    RooFit_data = RooDataSet("data", "data", {obsr})
+    for d in data:
+        obsr.setVal(d)
+        RooFit_data.add(RooArgSet(obsr))
+
+    minimizer = zfit.minimize.Minuit()
+
 Import the module with:
 
-.. code-block:: python
 
-    import zfit_physics.roofit as ztfroofit
 
-this will enable the RooFit functionality in zfit.
+.. jupyter-execute::
 
-We can create a RooFit NLL as ``RooFit_nll`` and use it as a loss function in zfit. For example, with a Gaussian model ``RooFit_gauss`` and a dataset ``RooFit_data``, both created with RooFit:
+    import zfit_physics.roofit as zroofit
+
+this will enable the RooFit functionality in zfit and allow to automatically minimize the function using a zfit minimimzer as
 
-.. code-block:: python
+.. jupyter-execute::
 
     RooFit_nll = RooFit_gauss.createNLL(RooFit_data)
-    minimizer.minimize(loss=RooFit_nll)
+
+We can create a RooFit NLL as ``RooFit_nll`` and use it as a loss function in zfit. For example, with a Gaussian model ``RooFit_gauss`` and a dataset ``RooFit_data``, both created with RooFit:
+
+.. jupyter-execute::
+
+    result = minimizer.minimize(loss=RooFit_nll)
 
 More explicitly, the loss function can be created with
 
-.. code-block:: python
+.. jupyter-execute::
 
-    nll = zroofit.loss.nll_from_roofit(fcn)
+    nll = zroofit.loss.nll_from_roofit(RooFit_nll)
 
 
 Variables

diff --git a/docs/api/static/zfit_physics.tfpwa.rst b/docs/api/static/zfit_physics.tfpwa.rst
@@ -1,7 +1,7 @@
 TF-PWA
 =======================
 
-TFPWA is a generic software package intended for Partial Wave Analysis (PWA). It can be connected with zfit,
+TF-PWA is a generic software package intended for Partial Wave Analysis (PWA). It can be connected with zfit,
 currently by providing a loss function that can be minimized by a zfit minimizer.
 
 Import the module with:
@@ -10,7 +10,7 @@ Import the module with:
 
     import zfit_physics.tfpwa as ztfpwa
 
-This will enable that :py:function:`~tfpwa.model.FCN` can be used as a loss function in zfit minimizers as
+This will enable that :py:class:`~tf_pwa.model.FCN` can be used as a loss function in zfit minimizers as
 
 .. code-block:: python
 

diff --git a/docs/api/zfit_physics.models.pdf_argus.rst b/docs/api/zfit_physics.models.pdf_argus.rst
diff --git a/docs/api/zfit_physics.models.pdf_cmsshape.rst b/docs/api/zfit_physics.models.pdf_cmsshape.rst
diff --git a/docs/api/zfit_physics.models.pdf_conv.rst b/docs/api/zfit_physics.models.pdf_conv.rst
diff --git a/docs/api/zfit_physics.models.pdf_cruijff.rst b/docs/api/zfit_physics.models.pdf_cruijff.rst
diff --git a/docs/api/zfit_physics.models.pdf_erfexp.rst b/docs/api/zfit_physics.models.pdf_erfexp.rst
diff --git a/docs/api/zfit_physics.models.pdf_example.rst b/docs/api/zfit_physics.models.pdf_example.rst
diff --git a/docs/api/zfit_physics.models.pdf_kde.rst b/docs/api/zfit_physics.models.pdf_kde.rst
diff --git a/docs/api/zfit_physics.models.pdf_novosibirsk.rst b/docs/api/zfit_physics.models.pdf_novosibirsk.rst
diff --git a/docs/api/zfit_physics.models.pdf_relbw.rst b/docs/api/zfit_physics.models.pdf_relbw.rst
diff --git a/docs/api/zfit_physics.models.pdf_tsallis.rst b/docs/api/zfit_physics.models.pdf_tsallis.rst
diff --git a/docs/api/zfit_physics.models.rst b/docs/api/zfit_physics.models.rst
diff --git a/docs/api/zfit_physics.pdf.rst b/docs/api/zfit_physics.pdf.rst
diff --git a/docs/api/zfit_physics.rst b/docs/api/zfit_physics.rst
diff --git a/docs/api/zfit_physics.unstable.pdf.rst b/docs/api/zfit_physics.unstable.pdf.rst
diff --git a/docs/api/zfit_physics.unstable.rst b/docs/api/zfit_physics.unstable.rst
diff --git a/docs/conf.py b/docs/conf.py
@@ -335,6 +335,11 @@
     "matplotlib": ("https://matplotlib.org/stable/", None),
     "pandas": ("https://pandas.pydata.org/docs/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/reference/", None),
+    "tensorwaves": ("https://tensorwaves.readthedocs.io/latest/", None),
+    "zfit": ("https://zfit.readthedocs.io/en/latest/", None),
+    "tf_pwa": ("https://tf-pwa.readthedocs.io/en/latest/", None),
+    "pyhf": ("https://pyhf.readthedocs.io/en/latest/", None),
 }
 
 # -- Options for todo extension ----------------------------------------------

diff --git a/docs/environment.yml b/docs/environment.yml
@@ -0,0 +1,10 @@
+name: rtd38
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - root<=6.30
+  - uv
+  - pip:
+      - ../[dev]
diff --git a/docs/make_docs.sh b/docs/make_docs.sh
@@ -6,11 +6,10 @@ MAKE_DOCS_PATH="$( cd "$(dirname "$0")" ; pwd -P )"
 popd > /dev/null
 
 # generate the ReST files
-echo "debug"
-echo ${MAKE_DOCS_PATH}/../zfit_physics
+#echo ${MAKE_DOCS_PATH}/../zfit_physics
 ls ${MAKE_DOCS_PATH}
 ls .
-sphinx-apidoc -o ${MAKE_DOCS_PATH}/api ${MAKE_DOCS_PATH}/../zfit_physics -fMeT && \
+sphinx-apidoc -o ${MAKE_DOCS_PATH}/api ${MAKE_DOCS_PATH}/../src/zfit_physics -fMeT && \
 python3 ${MAKE_DOCS_PATH}/api/tools/change_headline.py ${MAKE_DOCS_PATH}/api/zfit_physics.* && \
 make -C ${MAKE_DOCS_PATH} clean && make -C ${MAKE_DOCS_PATH} html -j8 && \
 echo "Documentation successfully built!" || echo "FAILED to build Documentation"
diff --git a/tests/roofit/test_loss_compat.py b/tests/roofit/test_loss_compat.py