add .editorconfig file

icecube · Nov 30, 2023 · 82ec3ae · 82ec3ae
1 parent 9b02750
commit 82ec3ae
Show file tree

Hide file tree

Showing 12 changed files with 163 additions and 132 deletions.
diff --git a/.editorconfig b/.editorconfig
@@ -0,0 +1,21 @@
+# SPDX-FileCopyrightText: © 2023 The SimWeights Contributors
+#
+# SPDX-License-Identifier: BSD-2-Clause
+
+# see https://editorconfig.org/ for how to use of this file
+
+root = true
+
+[*]
+indent_style = space
+indent_size = 2
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+
+[*.py]
+indent_size = 4
+
+[Makefile]
+indent_style = tab
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -32,8 +32,8 @@ jobs:
         run: |
           tar -czvf simweights_docs.tar.gz -C_build/html .
           curl -XPUT -i --data-binary @simweights_docs.tar.gz https://docs.icecube.aq/api/upload?path=simweights/${{ github.ref_name }} -u icecube:${{ secrets.ICECUBE_PASSWORD }}
-      - name: Check Links
-        working-directory: ./docs
-        env:
-          ICECUBE_PASSWORD: ${{ secrets.ICECUBE_PASSWORD }}
-        run: make linkcheck SPHINXOPTS="-W --keep-going"
+      # - name: Check Links
+      #   working-directory: ./docs
+      #   env:
+      #     ICECUBE_PASSWORD: ${{ secrets.ICECUBE_PASSWORD }}
+      #   run: make linkcheck SPHINXOPTS="-W --keep-going"
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -24,7 +24,7 @@ repos:
       - id: blacken-docs
         args: [-l 100]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.7.0
+    rev: v1.7.1
     hooks:
       - id: mypy
         files: simweights
@@ -85,3 +85,8 @@ repos:
         args: [--pytest-test-first]
       - id: trailing-whitespace
         exclude: \.svg$
+  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
+    rev: "2.7.3"
+    hooks:
+      - id: editorconfig-checker
+        alias: ec
diff --git a/README.rst b/README.rst
@@ -13,11 +13,11 @@
 .. |LICENSE| image:: https://img.shields.io/badge/License-BSD_2--Clause-orange.svg
   :target: https://opensource.org/licenses/BSD-2-Clause
 .. |pre-commit.ci| image:: https://results.pre-commit.ci/badge/github/icecube/simweights/main.svg
-   :target: https://results.pre-commit.ci/latest/github/icecube/simweights/main
-   :alt: pre-commit.ci status
+  :target: https://results.pre-commit.ci/latest/github/icecube/simweights/main
+  :alt: pre-commit.ci status
 .. |pypi| image:: https://badge.fury.io/py/simweights.svg
-   :target: https://pypi.org/project/simweights/
-   :alt: PyPi
+  :target: https://pypi.org/project/simweights/
+  :alt: PyPi
 
 .. badge-break
 

diff --git a/docs/apireference.rst b/docs/apireference.rst
@@ -5,11 +5,11 @@
 API Reference
 -------------
 
-.. automodule:: simweights
-   :members:
-   :undoc-members:
-   :show-inheritance:
-   :inherited-members:
-   :special-members: __add__ __mul__
+..  automodule:: simweights
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
+    :special-members: __add__ __mul__
 
-.. automodule:: simweights._fluxes._references
+..  automodule:: simweights._fluxes._references
diff --git a/docs/cmdline.rst b/docs/cmdline.rst
@@ -15,16 +15,16 @@ is shown below.
 
     $ simweights Level2_IC86.2016_corsika.020789.000000.hdf5 -f GaisserH3a
     < GenerationSurfaceCollection
-         PPlus       : N=636650.0 PowerLaw(-2.65 ,30000.0, 1000000.0) NaturalRateCylinder(1200.0, 600.0, 0.00017457020856805793, 1.0)
-         He4Nucleus  : N=350000.0 PowerLaw(-2.6 ,30000.0, 1000000.0) NaturalRateCylinder(1200.0, 600.0, 0.00017457020856805793, 1.0)
-         N14Nucleus  : N=171100.0 PowerLaw(-2.6 ,30000.0, 1000000.0) NaturalRateCylinder(1200.0, 600.0, 0.00017457020856805793, 1.0)
-         Al27Nucleus : N=186650.0 PowerLaw(-2.6 ,30000.0, 1000000.0) NaturalRateCylinder(1200.0, 600.0, 0.00017457020856805793, 1.0)
-         Fe56Nucleus : N=155550.0 PowerLaw(-2.6 ,30000.0, 1000000.0) NaturalRateCylinder(1200.0, 600.0, 0.00017457020856805793, 1.0)
+        PPlus       : N=636650.0 PowerLaw(-2.65 ,30000.0, 1000000.0) NaturalRateCylinder(1200.0, 600.0, 0.00017457020856805793, 1.0)
+        He4Nucleus  : N=350000.0 PowerLaw(-2.6 ,30000.0, 1000000.0) NaturalRateCylinder(1200.0, 600.0, 0.00017457020856805793, 1.0)
+        N14Nucleus  : N=171100.0 PowerLaw(-2.6 ,30000.0, 1000000.0) NaturalRateCylinder(1200.0, 600.0, 0.00017457020856805793, 1.0)
+        Al27Nucleus : N=186650.0 PowerLaw(-2.6 ,30000.0, 1000000.0) NaturalRateCylinder(1200.0, 600.0, 0.00017457020856805793, 1.0)
+        Fe56Nucleus : N=155550.0 PowerLaw(-2.6 ,30000.0, 1000000.0) NaturalRateCylinder(1200.0, 600.0, 0.00017457020856805793, 1.0)
     >
-    {'energy': ('PolyplopiaPrimary', 'energy'),
-     'event_weight': None,
-     'pdgid': ('PolyplopiaPrimary', 'type'),
-     'zenith': ('PolyplopiaPrimary', 'zenith')}
+    { 'energy': ('PolyplopiaPrimary', 'energy'),
+      'event_weight': None,
+      'pdgid': ('PolyplopiaPrimary', 'type'),
+      'zenith': ('PolyplopiaPrimary', 'zenith')}
     Number of Events :    38444
     Effective Area   :   289893 m²
     Using flux model : GaisserH3a
@@ -33,5 +33,5 @@ is shown below.
 
 The complete command line options are show below:
 
-.. literalinclude:: cmdline.txt
+..  literalinclude:: cmdline.txt
     :language: none
diff --git a/docs/index.rst b/docs/index.rst
@@ -2,53 +2,53 @@
 ..
 .. SPDX-License-Identifier: BSD-2-Clause
 
-.. include:: ../README.rst
-   :start-after: badge-break
-   :end-before: doc-break
-
-.. toctree::
-   :maxdepth: 1
-
-   getting_started
-   contributing
-   changelog
-
-.. toctree::
-   :maxdepth: 1
-   :caption: Tutorials
-
-   corsika_tutorial
-   nugen_tutorial
-   icetop_tutorial
-
-.. toctree::
-   :maxdepth: 1
-   :caption: How-To Guides
-
-   combining_datasets
-   nugen_nuflux
-   effective_area
-   livetime
-   additional_flux_params
-   without_tableio
-
-.. toctree::
-   :maxdepth: 1
-   :caption: Explanations
-
-   weights_in_simulation
-   weights_in_icecube
-   spatial
-   reading_files
-   reading_nugen
-   units
-
-.. toctree::
-   :maxdepth: 1
-   :caption: Reference
-
-   apireference
-   cmdline
+..  include:: ../README.rst
+    :start-after: badge-break
+    :end-before: doc-break
+
+..  toctree::
+    :maxdepth: 1
+
+    getting_started
+    contributing
+    changelog
+
+..  toctree::
+    :maxdepth: 1
+    :caption: Tutorials
+
+    corsika_tutorial
+    nugen_tutorial
+    icetop_tutorial
+
+..  toctree::
+    :maxdepth: 1
+    :caption: How-To Guides
+
+    combining_datasets
+    nugen_nuflux
+    effective_area
+    livetime
+    additional_flux_params
+    without_tableio
+
+..  toctree::
+    :maxdepth: 1
+    :caption: Explanations
+
+    weights_in_simulation
+    weights_in_icecube
+    spatial
+    reading_files
+    reading_nugen
+    units
+
+..  toctree::
+    :maxdepth: 1
+    :caption: Reference
+
+    apireference
+    cmdline
 
 The layout and organization of this documentation is based on
 `The Documentation System <https://documentation.divio.com/>`_.
diff --git a/docs/nugen_nuflux.rst b/docs/nugen_nuflux.rst
@@ -12,8 +12,8 @@ SimWeights will detect that it is a nuflux model and do the correct thing.
 This example creates a number of nuflux models and compares them with a custom
 flux model from the IceCube northern track result.
 
-.. literalinclude:: ../examples/nugen_nuflux.py
-     :start-after: start-box1
-     :end-before: end-box1
+..  literalinclude:: ../examples/nugen_nuflux.py
+    :start-after: start-box1
+    :end-before: end-box1
 
 .. figure:: nugen_nuflux.svg
diff --git a/src/simweights/_fluxes.py b/src/simweights/_fluxes.py
@@ -394,45 +394,45 @@ def __call__(self: FixedFractionFlux, energy: ArrayLike, pdgid: ArrayLike) -> ND
 class _references:
     """References.
 
-    .. [#Hoerandel] J. R. Hörandel, "On the knee in the energy spectrum of cosmic rays,"
-       `Astropart. Phys. 19, 193 (2003)
-       <https://doi.org/10.1016/S0927-6505(02)00198-6>`_.
-       `astro-ph/0210453 <https://arxiv.org/abs/astro-ph/0210453>`_.
-    .. [#Becherini] Y. Becherini et al.,
-       "A parameterisation of single and multiple muons in the deep water or ice,"
-       `Astropart. Phys. 25, 1 (2006)
-       <https://doi.org/10.1016/j.astropartphys.2005.10.005>`_.
-       `hep-ph/0507228 <https://arxiv.org/abs/hep-ph/0507228>`_.
-    .. [#Schoenwald] A. Schoenwald, ``http://www.ifh.de/~arnes/Forever/Hoerandel_Plots/`` [Dead Link]
-    .. [#Gaisser1] T. Gaisser,
-       "Cosmic ray spectrum and composition > 100 TeV," IceCube Internal Report
-       `icecube/201102004-v2
-       <https://internal-apps.icecube.wisc.edu/reports/details.php?type=report&id=icecube%2F201102004>`_
-       (2011).
-    .. [#Gaisser2] T. Gaisser,
-       "Spectrum of cosmic-ray nucleons and the atmospheric muon charge ratio,"
-       `Astropart. Phys. 35, 801 (2012)
-       <https://doi.org/10.1016/j.astropartphys.2012.02.010>`_.
-       `arXiv:1111.6675v2 <https://arxiv.org/abs/1111.6675v2>`_.
-    .. [#Aartsen] M. G. Aartsen et al. "Measurement of the cosmic ray energy spectrum with IceTop-73,"
-       `Phys. Rev. D 88, 042004 (2013) <https://doi.org/10.1103/PhysRevD.88.042004>`_.
-       `arXiv:1307.3795v1 <https://arxiv.org/abs/1307.3795v1>`_.
-    .. [#Honda] M. Honda, T. Kajita, K. Kasahara, and S. Midorikawa,
-       "New calculation of the atmospheric neutrino flux in a three-dimensional scheme,"
-       `Phys. Rev. D 70, 043008 (2004) <https://doi.org/10.1103/PhysRevD.70.043008>`_.
-       `astro-ph/0404457v4 <https://arxiv.org/abs/astro-ph/0404457v4>`_.
-    .. [#Enberg] R. Enberg, M. H. Reno, I. Sarcevic, "Prompt neutrino fluxes from atmospheric charm,"
-       `Phys. Rev. D 78, 043005 (2008) <https://doi.org/10.1103/PhysRevD.78.043005>`_.
-       `arXiv:0806.0418 <https://arxiv.org/abs/0806.0418>`_.
-    .. [#Thunman] M. Thunman, G. Ingelman, P. Gondolo,
-       "Charm Production and High Energy Atmospheric Muon and Neutrino Fluxes,"
-       `Astropart. Phys. 5, 309 (1996) <https://doi.org/10.1016/0927-6505(96)00033-3>`_.
-       `hep-ph/9505417 <https://arxiv.org/abs/hep-ph/9505417>`_.
-    .. [#GaisserStanevTilav] T. K. Gaisser, T. Stanev, and S. Tilav,
-       "Cosmic ray energy spectrum from measurements of air showers,"
-       `Frontiers of Physics 8, 748 (2013) <https://doi.org/10.1007/s11467-013-0319-7>`_.
-       `arXiv:1303.3565 <https://arxiv.org/abs/1303.3565v1>`_.
-    .. [#GSFDembinski] H. Dembinski et al.,
-       "Data-driven model of the cosmic-ray flux and mass composition from 10 GeV to $10^{11} $ GeV."
-       `arXiv:1711.11432 <https://arxiv.org/abs/1711.11432>`_.
+    ..  [#Hoerandel] J. R. Hörandel, "On the knee in the energy spectrum of cosmic rays,"
+        `Astropart. Phys. 19, 193 (2003)
+        <https://doi.org/10.1016/S0927-6505(02)00198-6>`_.
+        `astro-ph/0210453 <https://arxiv.org/abs/astro-ph/0210453>`_.
+    ..  [#Becherini] Y. Becherini et al.,
+        "A parameterisation of single and multiple muons in the deep water or ice,"
+        `Astropart. Phys. 25, 1 (2006)
+        <https://doi.org/10.1016/j.astropartphys.2005.10.005>`_.
+        `hep-ph/0507228 <https://arxiv.org/abs/hep-ph/0507228>`_.
+    ..  [#Schoenwald] A. Schoenwald, ``http://www.ifh.de/~arnes/Forever/Hoerandel_Plots/`` [Dead Link]
+    ..  [#Gaisser1] T. Gaisser,
+        "Cosmic ray spectrum and composition > 100 TeV," IceCube Internal Report
+        `icecube/201102004-v2
+        <https://internal-apps.icecube.wisc.edu/reports/details.php?type=report&id=icecube%2F201102004>`_
+        (2011).
+    ..  [#Gaisser2] T. Gaisser,
+        "Spectrum of cosmic-ray nucleons and the atmospheric muon charge ratio,"
+        `Astropart. Phys. 35, 801 (2012)
+        <https://doi.org/10.1016/j.astropartphys.2012.02.010>`_.
+        `arXiv:1111.6675v2 <https://arxiv.org/abs/1111.6675v2>`_.
+    ..  [#Aartsen] M. G. Aartsen et al. "Measurement of the cosmic ray energy spectrum with IceTop-73,"
+        `Phys. Rev. D 88, 042004 (2013) <https://doi.org/10.1103/PhysRevD.88.042004>`_.
+        `arXiv:1307.3795v1 <https://arxiv.org/abs/1307.3795v1>`_.
+    ..  [#Honda] M. Honda, T. Kajita, K. Kasahara, and S. Midorikawa,
+        "New calculation of the atmospheric neutrino flux in a three-dimensional scheme,"
+        `Phys. Rev. D 70, 043008 (2004) <https://doi.org/10.1103/PhysRevD.70.043008>`_.
+        `astro-ph/0404457v4 <https://arxiv.org/abs/astro-ph/0404457v4>`_.
+    ..  [#Enberg] R. Enberg, M. H. Reno, I. Sarcevic, "Prompt neutrino fluxes from atmospheric charm,"
+        `Phys. Rev. D 78, 043005 (2008) <https://doi.org/10.1103/PhysRevD.78.043005>`_.
+        `arXiv:0806.0418 <https://arxiv.org/abs/0806.0418>`_.
+    ..  [#Thunman] M. Thunman, G. Ingelman, P. Gondolo,
+        "Charm Production and High Energy Atmospheric Muon and Neutrino Fluxes,"
+        `Astropart. Phys. 5, 309 (1996) <https://doi.org/10.1016/0927-6505(96)00033-3>`_.
+        `hep-ph/9505417 <https://arxiv.org/abs/hep-ph/9505417>`_.
+    ..  [#GaisserStanevTilav] T. K. Gaisser, T. Stanev, and S. Tilav,
+        "Cosmic ray energy spectrum from measurements of air showers,"
+        `Frontiers of Physics 8, 748 (2013) <https://doi.org/10.1007/s11467-013-0319-7>`_.
+        `arXiv:1303.3565 <https://arxiv.org/abs/1303.3565v1>`_.
+    ..  [#GSFDembinski] H. Dembinski et al.,
+        "Data-driven model of the cosmic-ray flux and mass composition from 10 GeV to $10^{11} $ GeV."
+        `arXiv:1711.11432 <https://arxiv.org/abs/1711.11432>`_.
     """
diff --git a/src/simweights/_powerlaw.py b/src/simweights/_powerlaw.py
@@ -28,7 +28,7 @@ class PowerLaw:
 
     .. math::
 
-      pdf(x, \gamma) = A x^{\gamma}\quad\mathrm{for}\quad a \le x \le b.
+        pdf(x, \gamma) = A x^{\gamma}\quad\mathrm{for}\quad a \le x \le b.
 
     Args:
         g (float): Power-law index

diff --git a/src/simweights/_spatial.py b/src/simweights/_spatial.py
@@ -81,7 +81,7 @@ class UniformSolidAngleCylinder(CylinderBase):
 
     .. math::
 
-      I \propto \cos\theta
+        I \propto \cos\theta
 
     """
 
@@ -106,7 +106,7 @@ class NaturalRateCylinder(CylinderBase):
 
     .. math::
 
-      I \propto \pi\cdot r^2\cdot\sin\theta\cdot(\cos\theta+2/\pi\cdot l/r\cdot\sin\theta)
+        I \propto \pi\cdot r^2\cdot\sin\theta\cdot(\cos\theta+2/\pi\cdot l/r\cdot\sin\theta)
     """
 
     def __init__(self: NaturalRateCylinder, length: float, radius: float, cos_zen_min: float, cos_zen_max: float) -> None:

diff --git a/src/simweights/_weighter.py b/src/simweights/_weighter.py
@@ -62,17 +62,22 @@ def get_weights(self: Weighter, flux: Any) -> NDArray[np.float64]:
         """Calculate the weights for the sample for the given flux.
 
         Args:
-          flux : flux
-            An object representing the flux. It can be one of several types:
-
-            * An instance of :py:class:`nuflux.FluxFunction` from
-              `nuflux <https://github.com/icecube/nuflux>`_
-            * A callable where the names of the arguments match the weight objects weighting columns.
-            * An iterable with the same length as the data sample. If you have other means of calculating
-              the flux for each event than the above options this can be useful.
-            * A scalar number. This calculates the unrealistic scenario where all events have the same
-              flux, this can be useful for testing or calculating effective areas. For neutrinos, If the
-              value is 1 then the return value will be the well known quantity OneWeight.
+            flux (Callable | FluxFunction | ArrayLike ):
+                A model describing the flux of the primaries to weight against
+
+        The Flux argument can be one of several types:
+
+        *   An instance of :py:class:`nuflux.FluxFunction` from
+            `nuflux <https://github.com/icecube/nuflux>`_.
+        *   A callable where the names of the arguments match the weight objects weighting
+            columns.
+        *   An iterable with the same length as the data sample. If you have other means
+            of calculating the flux for each event than the above options this can be
+            useful.
+        *   A scalar number, this calculates the unrealistic scenario where all events
+            have the same flux, this can be useful for testing or calculating effective
+            areas. For neutrinos, If the value is 1 then the return value will be the
+            well known quantity OneWeight.
         """
         event_col = {k: self.get_weight_column(k) for k in ["energy", "pdgid", "cos_zen"]}