ref: make nanite pure Python

AFM-analysis · Jan 15, 2024 · 615427f · 615427f
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diff --git a/.github/workflows/check.yml b/.github/workflows/check.yml
@@ -25,7 +25,7 @@ jobs:
         python -m pip install --upgrade pip wheel
         python -m pip install coverage flake8 pytest
         # install dependencies
-        pip install -e .[CLI]
+        pip install -e .[ALL]
         # show installed packages
         pip freeze
     - name: Test with pytest

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -9,5 +9,5 @@ python:
     - method: pip
       path: .
       extra_requirements:
-        - CLI
+        - ALL
 
diff --git a/CHANGELOG b/CHANGELOG
@@ -1,3 +1,7 @@
+4.1.0
+ - ref: move to "src"-rooted source tree
+ - ref: move iterative `sneddon_spher` model to separate package which
+   makes nanite a pure Python package
 4.0.0
  - BREAKING CHANGE: Due to the new imputation of nan-valued features,
    rating inference might change slightly. For the "zef18" dataset,

diff --git a/nanite/model/model_sneddon_spherical.pyx b/nanite/model/model_sneddon_spherical.pyx
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,9 +1,5 @@
 [build-system]
-# Defined by PEP 518:
-# use oldest-supported-numpy (https://github.com/pypa/pip/issues/9542#issuecomment-771200755)
 requires = [
-    # for building Cython extensions
-    "cython", "oldest-supported-numpy", "setuptools", "wheel",
     # for version management
     "setuptools>=45", "setuptools_scm[toml]>=6.2"
 ]
@@ -46,6 +42,8 @@ CLI = ["appdirs",
        "matplotlib>=2.2.2",
        "tifffile>=0.15.0",
     ]
+ACA = ["nanite_model_sneddon_spher"]
+ALL = ["nanite[CLI,ACA]"]
 
 [project.scripts]
 nanite-setup-profile = "nanite.cli:setup_profile [CLI]"
@@ -59,12 +57,7 @@ tracker = "https://github.com/AFM-Analysis/nanite/issues"
 documentation = "https://nanite.readthedocs.io/en/stable/"
 changelog = "https://nanite.readthedocs.io/en/stable/sec_changelog.html"
 
-# We need the following, because automatic package discovery does not work
-# when running cibuildwheel on GitHub Actions (there will be a "wheelhouse"
-# directory).
-[tool.setuptools]
-packages = ["nanite"]
 
 [tool.setuptools_scm]
-write_to = "nanite/_version.py"
+write_to = "src/nanite/_version.py"
 version_scheme = "post-release"
diff --git a/setup.py b/setup.py
diff --git a/nanite/__init__.py → src/nanite/__init__.py b/nanite/__init__.py → src/nanite/__init__.py
diff --git a/nanite/cli/__init__.py → src/nanite/cli/__init__.py b/nanite/cli/__init__.py → src/nanite/cli/__init__.py
diff --git a/nanite/cli/plotting.py → src/nanite/cli/plotting.py b/nanite/cli/plotting.py → src/nanite/cli/plotting.py
diff --git a/nanite/cli/profile.py → src/nanite/cli/profile.py b/nanite/cli/profile.py → src/nanite/cli/profile.py
diff --git a/nanite/cli/rating.py → src/nanite/cli/rating.py b/nanite/cli/rating.py → src/nanite/cli/rating.py
diff --git a/nanite/fit.py → src/nanite/fit.py b/nanite/fit.py → src/nanite/fit.py
diff --git a/nanite/group.py → src/nanite/group.py b/nanite/group.py → src/nanite/group.py
diff --git a/nanite/indent.py → src/nanite/indent.py b/nanite/indent.py → src/nanite/indent.py
diff --git a/nanite/model/__init__.py → src/nanite/model/__init__.py b/nanite/model/__init__.py → src/nanite/model/__init__.py
@@ -3,14 +3,21 @@
 from . import model_conical_indenter  # noqa: F401
 from . import model_hertz_paraboloidal  # noqa: F401
 from . import model_hertz_three_sided_pyramid  # noqa: F401
-from . import model_sneddon_spherical  # noqa: F401
 from . import model_sneddon_spherical_approximation  # noqa: F401
 
 from .core import NaniteFitModel  # noqa: F401
 from . import residuals  # noqa: F401
 from .logic import models_available, register_model
 from .logic import deregister_model, load_model_from_file  # noqa: F401
 
+try:
+    # Since version 4.1.0, the iterative sneddon_spher model is not
+    # part of nanite anymore.
+    from nanite_model_sneddon_spher import \
+        model_sneddon_spherical  # noqa: F401
+except (ImportError, MemoryError):
+    pass
+
 
 def compute_anc_parms(idnt, model_key):
     """Compute ancillary parameters for a force-distance dataset

diff --git a/nanite/model/core.py → src/nanite/model/core.py b/nanite/model/core.py → src/nanite/model/core.py
diff --git a/nanite/model/logic.py → src/nanite/model/logic.py b/nanite/model/logic.py → src/nanite/model/logic.py
diff --git a/nanite/model/model_conical_indenter.py → src/nanite/model/model_conical_indenter.py b/nanite/model/model_conical_indenter.py → src/nanite/model/model_conical_indenter.py
diff --git a/nanite/model/model_hertz_paraboloidal.py → src/nanite/model/model_hertz_paraboloidal.py b/nanite/model/model_hertz_paraboloidal.py → src/nanite/model/model_hertz_paraboloidal.py
diff --git a/.../model/model_hertz_three_sided_pyramid.py → .../model/model_hertz_three_sided_pyramid.py b/.../model/model_hertz_three_sided_pyramid.py → .../model/model_hertz_three_sided_pyramid.py
diff --git a/.../model_sneddon_spherical_approximation.py → .../model_sneddon_spherical_approximation.py b/.../model_sneddon_spherical_approximation.py → .../model_sneddon_spherical_approximation.py
diff --git a/nanite/model/residuals.py → src/nanite/model/residuals.py b/nanite/model/residuals.py → src/nanite/model/residuals.py
diff --git a/nanite/model/weight.py → src/nanite/model/weight.py b/nanite/model/weight.py → src/nanite/model/weight.py
diff --git a/nanite/poc.py → src/nanite/poc.py b/nanite/poc.py → src/nanite/poc.py
diff --git a/nanite/preproc.py → src/nanite/preproc.py b/nanite/preproc.py → src/nanite/preproc.py
diff --git a/nanite/qmap.py → src/nanite/qmap.py b/nanite/qmap.py → src/nanite/qmap.py
diff --git a/nanite/rate/__init__.py → src/nanite/rate/__init__.py b/nanite/rate/__init__.py → src/nanite/rate/__init__.py
diff --git a/nanite/rate/features.py → src/nanite/rate/features.py b/nanite/rate/features.py → src/nanite/rate/features.py
diff --git a/nanite/rate/io.py → src/nanite/rate/io.py b/nanite/rate/io.py → src/nanite/rate/io.py
diff --git a/nanite/rate/rater.py → src/nanite/rate/rater.py b/nanite/rate/rater.py → src/nanite/rate/rater.py
diff --git a/nanite/rate/regressors.py → src/nanite/rate/regressors.py b/nanite/rate/regressors.py → src/nanite/rate/regressors.py
diff --git a/...zef18/train_feat_bin_apr_spikes_count.txt → ...zef18/train_feat_bin_apr_spikes_count.txt b/...zef18/train_feat_bin_apr_spikes_count.txt → ...zef18/train_feat_bin_apr_spikes_count.txt
diff --git a/...e/ts_zef18/train_feat_bin_cp_position.txt → ...e/ts_zef18/train_feat_bin_cp_position.txt b/...e/ts_zef18/train_feat_bin_cp_position.txt → ...e/ts_zef18/train_feat_bin_cp_position.txt
diff --git a/nanite/rate/ts_zef18/train_feat_bin_size.txt → ...ite/rate/ts_zef18/train_feat_bin_size.txt b/nanite/rate/ts_zef18/train_feat_bin_size.txt → ...ite/rate/ts_zef18/train_feat_bin_size.txt
diff --git a/.../ts_zef18/train_feat_con_apr_flatness.txt → .../ts_zef18/train_feat_con_apr_flatness.txt b/.../ts_zef18/train_feat_con_apr_flatness.txt → .../ts_zef18/train_feat_con_apr_flatness.txt
diff --git a/...rate/ts_zef18/train_feat_con_apr_size.txt → ...rate/ts_zef18/train_feat_con_apr_size.txt b/...rate/ts_zef18/train_feat_con_apr_size.txt → ...rate/ts_zef18/train_feat_con_apr_size.txt
diff --git a/.../rate/ts_zef18/train_feat_con_apr_sum.txt → .../rate/ts_zef18/train_feat_con_apr_sum.txt b/.../rate/ts_zef18/train_feat_con_apr_sum.txt → .../rate/ts_zef18/train_feat_con_apr_sum.txt
diff --git a/...ate/ts_zef18/train_feat_con_bln_slope.txt → ...ate/ts_zef18/train_feat_con_bln_slope.txt b/...ate/ts_zef18/train_feat_con_bln_slope.txt → ...ate/ts_zef18/train_feat_con_bln_slope.txt
diff --git a/...ts_zef18/train_feat_con_bln_variation.txt → ...ts_zef18/train_feat_con_bln_variation.txt b/...ts_zef18/train_feat_con_bln_variation.txt → ...ts_zef18/train_feat_con_bln_variation.txt
diff --git a/.../ts_zef18/train_feat_con_cp_curvature.txt → .../ts_zef18/train_feat_con_cp_curvature.txt b/.../ts_zef18/train_feat_con_cp_curvature.txt → .../ts_zef18/train_feat_con_cp_curvature.txt
diff --git a/.../ts_zef18/train_feat_con_cp_magnitude.txt → .../ts_zef18/train_feat_con_cp_magnitude.txt b/.../ts_zef18/train_feat_con_cp_magnitude.txt → .../ts_zef18/train_feat_con_cp_magnitude.txt
diff --git a/...ef18/train_feat_con_idt_maxima_75perc.txt → ...ef18/train_feat_con_idt_maxima_75perc.txt b/...ef18/train_feat_con_idt_maxima_75perc.txt → ...ef18/train_feat_con_idt_maxima_75perc.txt
diff --git a/.../ts_zef18/train_feat_con_idt_monotony.txt → .../ts_zef18/train_feat_con_idt_monotony.txt b/.../ts_zef18/train_feat_con_idt_monotony.txt → .../ts_zef18/train_feat_con_idt_monotony.txt
diff --git a/...s_zef18/train_feat_con_idt_spike_area.txt → ...s_zef18/train_feat_con_idt_spike_area.txt b/...s_zef18/train_feat_con_idt_spike_area.txt → ...s_zef18/train_feat_con_idt_spike_area.txt
diff --git a/.../rate/ts_zef18/train_feat_con_idt_sum.txt → .../rate/ts_zef18/train_feat_con_idt_sum.txt b/.../rate/ts_zef18/train_feat_con_idt_sum.txt → .../rate/ts_zef18/train_feat_con_idt_sum.txt
diff --git a/...s_zef18/train_feat_con_idt_sum_75perc.txt → ...s_zef18/train_feat_con_idt_sum_75perc.txt b/...s_zef18/train_feat_con_idt_sum_75perc.txt → ...s_zef18/train_feat_con_idt_sum_75perc.txt
diff --git a/nanite/rate/ts_zef18/train_response.txt → src/nanite/rate/ts_zef18/train_response.txt b/nanite/rate/ts_zef18/train_response.txt → src/nanite/rate/ts_zef18/train_response.txt
diff --git a/nanite/read.py → src/nanite/read.py b/nanite/read.py → src/nanite/read.py
diff --git a/nanite/smooth.py → src/nanite/smooth.py b/nanite/smooth.py → src/nanite/smooth.py
-Original file line number
+Diff line change
@@ Expand Up / @@ -9,5 +9,5 @@ python: @@
         - method: pip
           path: .
           extra_requirements:
-            - CLI
+            - ALL