Merged dev-4-0-1 branch

CHANGELOG.md

@@ -1,3 +1,8 @@
+# 4.0.1 (2023/03/22)
+
+- Updated how `perform_exploratory_tests` handles cases where all mu values are greater than the mu-criterion.
+
+
 # 4.0.0 (2023/03/20)
 
 **THIS UPDATE CONTAINS SEVERAL CHANGES THAT ARE NOT BACKWARDS COMPATIBLE WITH CODE WRITTEN USING VERSION 3.x!**

build.sh

@@ -82,6 +82,13 @@ validate_wheel
 # Update documentation
 # - The contents of './docs/build/html' should be committed to the gh-pages branch
 # - ./docs/build/latex/latex/pyimpspec.pdf should be uploaded as an attachment to a release
+# Update documentation
+# - The contents of ./dist/html should be committed to the gh-pages branch
+#   - Run the reset.sh script found in gh-pages
+#   - Copy the files from ./dist/html
+#   - Commit
+#   - Force push
+# - ./dist/pyimpspec-X-Y-Z.pdf should be uploaded as an attachment to a release
 echo
 echo "Generating documentation..."
 # Generate HTML, run tests, and finally generate PDF

docs/README.md

@@ -0,0 +1,4 @@
+# Documentation
+
+The documentation is generated via `build.sh` from the repository root.
+Images are stored in the wiki repository: https://github.com/vyrjana/pyimpspec.wiki.git

docs/source/index.rst

@@ -29,23 +29,31 @@ Welcome to pyimpspec's documentation!
       :alt: PyPI
       :target: https://pypi.org/project/pyimpspec/
 
-
 Pyimpspec is a Python package for processing, analyzing, and visualizing impedance spectra.
+
+.. figure:: https://raw.githubusercontent.com/wiki/vyrjana/pyimpspec/images/kramers-kronig.png
+   :alt: Kramers-Kronig test results
+
+
 The primary interface for using pyimpspec is the application programming interface (API).
 
 .. doctest::
 
    >>> import pyimpspec
 
+
 A command-line interface (CLI) is also included to provide a way to, e.g., quickly plot some experimental data via a terminal.
 
 .. code:: bash
 
    # The CLI should be accessible in the terminal in the following ways
-   pyimpspec --version
-   python -m pyimpspec --version
+   pyimpspec
+   python -m pyimpspec
+
 
+If you would prefer to use a graphical user interface (GUI), then check out `DearEIS <https://vyrjana.github.io/DearEIS>`_.
 
+The source code for pyimpspec can be found `here <https://github.com/vyrjana/pyimpspec>`_.
 The changelog can be found `here <https://github.com/vyrjana/pyimpspec/blob/main/CHANGELOG.md>`_.
 If you encounter bugs or wish to request a feature, then please open an `issue on GitHub <https://github.com/vyrjana/pyimpspec/issues>`_.
 If you wish to contribute to the project, then please read the `readme <https://github.com/vyrjana/pyimpspec/blob/main/README.md>`_ before submitting a `pull request via GitHub <https://github.com/vyrjana/pyimpspec/pulls>`_.

post-build.py

@@ -4,7 +4,6 @@
     walk,
 )
 from os.path import (
-    basename,
     exists,
     isdir,
     join,
@@ -38,7 +37,7 @@ def copy_html(src: str, dst: str):
             ".pdf",
         )
     ]
-    dirs: List[str] = ["_images", "_static"]
+    dirs: List[str] = ["_images", "_static", "_sources"]
     if not isdir(dst):
         makedirs(dst)
     name: str
@@ -48,15 +47,13 @@ def copy_html(src: str, dst: str):
         copytree(join(src, name), join(dst, name))
 
 
-def copy_pdf(src: str, dst: str, version_path: str):
+def copy_pdf(src: str, dst: str, name: str, version_path: str):
     version: str = ""
     with open(version_path, "r") as fp:
         version = fp.read().strip().replace(".", "-")
     assert version != ""
-    name: str
-    ext: str
-    name, ext = splitext(basename(src))
-    dst = join(dst, f"{name} - {version}{ext}")
+    ext: str = splitext(src)[1]
+    dst = join(dst, f"{name}-{version}{ext}")
     if exists(dst):
         remove(dst)
     copy(src, dst)
@@ -70,5 +67,6 @@ def copy_pdf(src: str, dst: str, version_path: str):
     copy_pdf(
         src="./docs/build/latex/latex/pyimpspec.pdf",
         dst="./dist",
+        name="pyimpspec",
         version_path="./version.txt",
     )

setup.py

@@ -40,7 +40,7 @@
     "dev": dev_dependencies,
 }
 
-version = "4.0.0"
+version = "4.0.1"
 
 if __name__ == "__main__":
     with open("requirements.txt", "w") as fp:

src/pyimpspec/analysis/kramers_kronig.py

@@ -39,6 +39,7 @@
     floating,
     inf,
     integer,
+    isinf,
     issubdtype,
     log10 as log,
     min,
@@ -1448,8 +1449,12 @@ def perform_exploratory_tests(
                 residuals=_calculate_residuals(Z_exp, Z_fit),
             )
         )
-    results.sort(
-        key=lambda _: _.calculate_score(mu_criterion),
-        reverse=True,
-    )
+    scores: List[float] = [_.calculate_score(mu_criterion) for _ in results]
+    if all(map(isinf, scores)):
+        results.sort(key=lambda _: abs(-6 - log(_.pseudo_chisqr)))
+    else:
+        results.sort(
+            key=lambda _: _.calculate_score(mu_criterion),
+            reverse=True,
+        )
     return results

src/pyimpspec/version.py

@@ -17,4 +17,4 @@
 # The licenses of pyimpspec's dependencies and/or sources of portions of code are included in
 # the LICENSES folder.
 
-PACKAGE_VERSION: str = "4.0.0"
+PACKAGE_VERSION: str = "4.0.1"

version.txt

@@ -1 +1 @@
-4.0.0
+4.0.1