Merge branch 'master' into joss-paper

Author: MarJMue

.github/workflows/build-docker.yml

@@ -14,19 +14,19 @@ jobs:
         with:
           submodules: recursive
       - name: Log in to Docker Hub
-        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        uses: docker/login-action@74a5d142397b4f367a81961eba4e8cd7edddf772
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        uses: docker/metadata-action@902fa8ec7d6ecbf8d84d538b9b233a880e428804
         with:
           images: domna/pyelli
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        uses: docker/build-push-action@1dc73863535b631f98b2378be8619f83b136f4a0
         with:
           context: .
           push: true

AUTHORS.md

@@ -1,7 +1,7 @@
 # Contributors
 
-- Marius Müller <marius.mueller@physik.uni-giessen.de>
-- Florian Dobener <[email protected]>
+- Marius Müller <marius.mueller@tutanota.de>
+- Florian Dobener <[email protected]>
 
 # Acknowledgements
 

CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changelog
 
+## Version 0.22.3
+
+### Bugfixes
+
+- Pin Plotly to a version smaller than 6, to avoid problems with the fitting widget (#203).
+
 ## Version 0.22.2
 
 ### Bugfixes

README.md

@@ -84,4 +84,4 @@ Until we have published a Paper on pyElli, we have prepared a Zenodo entry with
 - Solver2x2 based on Steve Byrnes' [tmm](https://github.com/sbyrnes321/tmm)
 - Mikhail Polyanskiy's [refractiveindex.info database](https://github.com/polyanskiy/refractiveindex.info-database) and Pavel Dmitriev's [pyTMM](https://github.com/kitchenknif/PyTMM) for his importer script for the database
 
-[@MarJMue](https://github.com/MarJMue) receives financial support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation), grant No. 398143140 (FOR 2824).
+[@MarJMue](https://github.com/MarJMue) received financial support from 2021 until 2025 by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation), grant No. 398143140 (FOR 2824).

docs/requirements.txt

@@ -7,7 +7,7 @@ name = "pyElli"
 description = "An ellipsometry analysis tool for reproducible and comprehensible building of optical models."
 dynamic = ["version"]
 authors = [
-    { name = "Marius Müller", email = "marius.mueller@physik.uni-giessen.de" },
+    { name = "Marius Müller", email = "marius.mueller@tutanota.de" },
     { name = "Florian Dobener", email = "[email protected]" },
 ]
 requires-python = ">=3.9"
@@ -40,7 +40,7 @@ fitting = [
     "ipython",
     "ipywidgets",
     "anywidget",
-    "plotly",
+    "plotly<6",
     "matplotlib",
     "lmfit",
 ]
@@ -53,6 +53,15 @@ dev = [
     "uv",
     "pre-commit",
 ]
+docs = [
+    "sphinx!=5.1.0",
+    "sphinx_rtd_theme",
+    "sphinx-mdinclude",
+    "sphinx-gallery",
+    "sphinx-plotly-directive",
+    "sphinxcontrib-mermaid",
+    "myst_parser",
+]
 
 [project.urls]
 homepage = "https://github.com/PyEllips/pyElli/"

pyproject.toml

@@ -214,6 +214,13 @@ distlib==0.3.9 \
     --hash=sha256:47f8c22fd27c27e25a65601af709b38e4f0a45ea4fc2e710f65755fa8caaaf87 \
     --hash=sha256:a60f20dea646b8a33f3e7772f74dc0b2d0772d2837ee1342a00645c81edf9403
     # via virtualenv
+exceptiongroup==1.2.2 \
+    --hash=sha256:3111b9d131c238bec2f8f516e123e14ba243563fb135d3fe885990585aa7795b \
+    --hash=sha256:47c2edf7c6738fafb49fd34290706d1a1a2f4d1c6df275526b62cbb4aa5393cc
+    # via
+    #   -r requirements/fitting-requirements.txt
+    #   ipython
+    #   pytest
 executing==2.2.0 \
     --hash=sha256:11387150cad388d62750327a53d3339fad4888b39a6fe233c3afbb54ecffd3aa \
     --hash=sha256:5d108c028108fe2551d1a7b2e8b713341e2cb4fc0aa7dcf966fa4327a5226755
@@ -342,20 +349,14 @@ ipykernel==6.29.5 \
     --hash=sha256:afdb66ba5aa354b09b91379bac28ae4afebbb30e8b39510c9690afb7a10421b5 \
     --hash=sha256:f093a22c4a40f8828f8e330a9c297cb93dcab13bd9678ded6de8e5cf81c56215
     # via nbmake
-ipython==9.0.2 \
-    --hash=sha256:143ef3ea6fb1e1bffb4c74b114051de653ffb7737a3f7ab1670e657ca6ae8c44 \
-    --hash=sha256:ec7b479e3e5656bf4f58c652c120494df1820f4f28f522fb7ca09e213c2aab52
+ipython==8.34.0 \
+    --hash=sha256:0419883fa46e0baa182c5d50ebb8d6b49df1889fdb70750ad6d8cfe678eda6e3 \
+    --hash=sha256:c31d658e754673ecc6514583e7dda8069e47136eb62458816b7d1e6625948b5a
     # via
     #   -r requirements/fitting-requirements.txt
     #   pyelli (pyproject.toml)
     #   ipykernel
     #   ipywidgets
-ipython-pygments-lexers==1.1.1 \
-    --hash=sha256:09c0138009e56b6854f9535736f4171d855c8c08a563a0dcd8022f78355c7e81 \
-    --hash=sha256:a9462224a505ade19a605f71f8fa63c2048833ce50abc86768a0d81d876dc81c
-    # via
-    #   -r requirements/fitting-requirements.txt
-    #   ipython
 ipywidgets==8.1.5 \
     --hash=sha256:3290f526f87ae6e77655555baba4f36681c555b8bdbbff430b70e52c34c86245 \
     --hash=sha256:870e43b1a35656a80c18c9503bbf2d16802db1cb487eec6fab27d683381dde17
@@ -538,12 +539,6 @@ matplotlib-inline==0.1.7 \
     #   -r requirements/fitting-requirements.txt
     #   ipykernel
     #   ipython
-narwhals==1.29.1 \
-    --hash=sha256:2f68cfbb2562672c4dfa54f158ed8c2828e9920ef784981cd9114e419c444216 \
-    --hash=sha256:c408acf09e90c116f247cf34f24a3a89d147e3e235b1d3c708cfd1960baf320a
-    # via
-    #   -r requirements/fitting-requirements.txt
-    #   plotly
 nbclient==0.10.2 \
     --hash=sha256:4ffee11e788b4a27fabeb7955547e4318a5298f34342a4bfd01f2e1faaeadc3d \
     --hash=sha256:90b7fc6b810630db87a6d0c2250b1f0ab4cf4d3c27a299b0cde78a4ed3fd9193
@@ -787,9 +782,9 @@ platformdirs==4.3.6 \
     #   jupyter-core
     #   pint
     #   virtualenv
-plotly==6.0.0 \
-    --hash=sha256:c4aad38b8c3d65e4a5e7dd308b084143b9025c2cc9d5317fc1f1d30958db87d3 \
-    --hash=sha256:f708871c3a9349a68791ff943a5781b1ec04de7769ea69068adcd9202e57653a
+plotly==5.24.1 \
+    --hash=sha256:dbc8ac8339d248a4bcc36e08a5659bacfe1b079390b8953533f4eb22169b4bae \
+    --hash=sha256:f67073a1e637eb0dc3e46324d9d51e2fe76e9727c892dde64ddf1e1b51f29089
     # via
     #   -r requirements/fitting-requirements.txt
     #   pyelli (pyproject.toml)
@@ -872,7 +867,6 @@ pygments==2.19.1 \
     # via
     #   -r requirements/fitting-requirements.txt
     #   ipython
-    #   ipython-pygments-lexers
     #   nbmake
 pyparsing==3.2.1 \
     --hash=sha256:506ff4f4386c4cec0590ec19e6302d3aedb992fdc02c761e90416f158dacf8e1 \
@@ -1375,18 +1369,61 @@ stack-data==0.6.3 \
     # via
     #   -r requirements/fitting-requirements.txt
     #   ipython
-tornado==6.4.2 \
-    --hash=sha256:072ce12ada169c5b00b7d92a99ba089447ccc993ea2143c9ede887e0937aa803 \
-    --hash=sha256:1a017d239bd1bb0919f72af256a970624241f070496635784d9bf0db640d3fec \
-    --hash=sha256:2876cef82e6c5978fde1e0d5b1f919d756968d5b4282418f3146b79b58556482 \
-    --hash=sha256:304463bd0772442ff4d0f5149c6f1c2135a1fae045adf070821c6cdc76980634 \
-    --hash=sha256:908b71bf3ff37d81073356a5fadcc660eb10c1476ee6e2725588626ce7e5ca38 \
-    --hash=sha256:92bad5b4746e9879fd7bf1eb21dce4e3fc5128d71601f80005afa39237ad620b \
-    --hash=sha256:932d195ca9015956fa502c6b56af9eb06106140d844a335590c1ec7f5277d10c \
-    --hash=sha256:bca9eb02196e789c9cb5c3c7c0f04fb447dc2adffd95265b2c7223a8a615ccbf \
-    --hash=sha256:c36e62ce8f63409301537222faffcef7dfc5284f27eec227389f2ad11b09d946 \
-    --hash=sha256:c82c46813ba483a385ab2a99caeaedf92585a1f90defb5693351fa7e4ea0bf73 \
-    --hash=sha256:e828cce1123e9e44ae2a50a9de3055497ab1d0aeb440c5ac23064d9e44880da1
+tenacity==9.0.0 \
+    --hash=sha256:807f37ca97d62aa361264d497b0e31e92b8027044942bfa756160d908320d73b \
+    --hash=sha256:93de0c98785b27fcf659856aa9f54bfbd399e29969b0621bc7f762bd441b4539
+    # via
+    #   -r requirements/fitting-requirements.txt
+    #   plotly
+tomli==2.2.1 \
+    --hash=sha256:023aa114dd824ade0100497eb2318602af309e5a55595f76b626d6d9f3b7b0a6 \
+    --hash=sha256:02abe224de6ae62c19f090f68da4e27b10af2b93213d36cf44e6e1c5abd19fdd \
+    --hash=sha256:286f0ca2ffeeb5b9bd4fcc8d6c330534323ec51b2f52da063b11c502da16f30c \
+    --hash=sha256:2d0f2fdd22b02c6d81637a3c95f8cd77f995846af7414c5c4b8d0545afa1bc4b \
+    --hash=sha256:33580bccab0338d00994d7f16f4c4ec25b776af3ffaac1ed74e0b3fc95e885a8 \
+    --hash=sha256:400e720fe168c0f8521520190686ef8ef033fb19fc493da09779e592861b78c6 \
+    --hash=sha256:40741994320b232529c802f8bc86da4e1aa9f413db394617b9a256ae0f9a7f77 \
+    --hash=sha256:465af0e0875402f1d226519c9904f37254b3045fc5084697cefb9bdde1ff99ff \
+    --hash=sha256:4a8f6e44de52d5e6c657c9fe83b562f5f4256d8ebbfe4ff922c495620a7f6cea \
+    --hash=sha256:4e340144ad7ae1533cb897d406382b4b6fede8890a03738ff1683af800d54192 \
+    --hash=sha256:678e4fa69e4575eb77d103de3df8a895e1591b48e740211bd1067378c69e8249 \
+    --hash=sha256:6972ca9c9cc9f0acaa56a8ca1ff51e7af152a9f87fb64623e31d5c83700080ee \
+    --hash=sha256:7fc04e92e1d624a4a63c76474610238576942d6b8950a2d7f908a340494e67e4 \
+    --hash=sha256:889f80ef92701b9dbb224e49ec87c645ce5df3fa2cc548664eb8a25e03127a98 \
+    --hash=sha256:8d57ca8095a641b8237d5b079147646153d22552f1c637fd3ba7f4b0b29167a8 \
+    --hash=sha256:8dd28b3e155b80f4d54beb40a441d366adcfe740969820caf156c019fb5c7ec4 \
+    --hash=sha256:9316dc65bed1684c9a98ee68759ceaed29d229e985297003e494aa825ebb0281 \
+    --hash=sha256:a198f10c4d1b1375d7687bc25294306e551bf1abfa4eace6650070a5c1ae2744 \
+    --hash=sha256:a38aa0308e754b0e3c67e344754dff64999ff9b513e691d0e786265c93583c69 \
+    --hash=sha256:a92ef1a44547e894e2a17d24e7557a5e85a9e1d0048b0b5e7541f76c5032cb13 \
+    --hash=sha256:ac065718db92ca818f8d6141b5f66369833d4a80a9d74435a268c52bdfa73140 \
+    --hash=sha256:b82ebccc8c8a36f2094e969560a1b836758481f3dc360ce9a3277c65f374285e \
+    --hash=sha256:c954d2250168d28797dd4e3ac5cf812a406cd5a92674ee4c8f123c889786aa8e \
+    --hash=sha256:cb55c73c5f4408779d0cf3eef9f762b9c9f147a77de7b258bef0a5628adc85cc \
+    --hash=sha256:cd45e1dc79c835ce60f7404ec8119f2eb06d38b1deba146f07ced3bbc44505ff \
+    --hash=sha256:d3f5614314d758649ab2ab3a62d4f2004c825922f9e370b29416484086b264ec \
+    --hash=sha256:d920f33822747519673ee656a4b6ac33e382eca9d331c87770faa3eef562aeb2 \
+    --hash=sha256:db2b95f9de79181805df90bedc5a5ab4c165e6ec3fe99f970d0e302f384ad222 \
+    --hash=sha256:e59e304978767a54663af13c07b3d1af22ddee3bb2fb0618ca1593e4f593a106 \
+    --hash=sha256:e85e99945e688e32d5a35c1ff38ed0b3f41f43fad8df0bdf79f72b2ba7bc5272 \
+    --hash=sha256:ece47d672db52ac607a3d9599a9d48dcb2f2f735c6c2d1f34130085bb12b112a \
+    --hash=sha256:f4039b9cbc3048b2416cc57ab3bda989a6fcf9b36cf8937f01a6e731b64f80d7
+    # via
+    #   coverage
+    #   pytest
+tornado==6.5.1 \
+    --hash=sha256:02420a0eb7bf617257b9935e2b754d1b63897525d8a289c9d65690d580b4dcf7 \
+    --hash=sha256:13ce6e3396c24e2808774741331638ee6c2f50b114b97a55c5b442df65fd9692 \
+    --hash=sha256:253b76040ee3bab8bcf7ba9feb136436a3787208717a1fb9f2c16b744fba7331 \
+    --hash=sha256:308473f4cc5a76227157cdf904de33ac268af770b2c5f05ca6c1161d82fdd95e \
+    --hash=sha256:5cae6145f4cdf5ab24744526cc0f55a17d76f02c98f4cff9daa08ae9a217448a \
+    --hash=sha256:84ceece391e8eb9b2b95578db65e920d2a61070260594819589609ba9bc6308c \
+    --hash=sha256:908e7d64567cecd4c2b458075589a775063453aeb1d2a1853eedb806922f568b \
+    --hash=sha256:9e9ca370f717997cb85606d074b0e5b247282cf5e2e1611568b8821afe0342d6 \
+    --hash=sha256:b77e9dfa7ed69754a54c89d82ef746398be82f749df69c4d3abe75c4d1ff4888 \
+    --hash=sha256:caec6314ce8a81cf69bd89909f4b633b9f523834dc1a352021775d45e51d9401 \
+    --hash=sha256:d50065ba7fd11d3bd41bcad0825227cc9a95154bad83239357094c36708001f7 \
+    --hash=sha256:e0a36e1bc684dca10b1aa75a31df8bdfed656831489bc1e6a6ebed05dc1ec365
     # via
     #   ipykernel
     #   jupyter-client
@@ -1412,7 +1449,9 @@ typing-extensions==4.12.2 \
     #   anywidget
     #   flexcache
     #   flexparser
+    #   ipython
     #   pint
+    #   referencing
 tzdata==2025.1 \
     --hash=sha256:24894909e88cdb28bd1636c6887801df64cb485bd593f2fd83ef29075a81d694 \
     --hash=sha256:7e127113816800496f027041c570f50bcd464a020098a3b6b199517772303639

requirements/dev-requirements.txt

@@ -90,6 +90,10 @@ dill==0.3.9 \
     --hash=sha256:468dff3b89520b474c0397703366b7b95eebe6303f108adf9b19da1f702be87a \
     --hash=sha256:81aa267dddf68cbfe8029c42ca9ec6a4ab3b22371d1c450abc54422577b4512c
     # via lmfit
+exceptiongroup==1.2.2 \
+    --hash=sha256:3111b9d131c238bec2f8f516e123e14ba243563fb135d3fe885990585aa7795b \
+    --hash=sha256:47c2edf7c6738fafb49fd34290706d1a1a2f4d1c6df275526b62cbb4aa5393cc
+    # via ipython
 executing==2.2.0 \
     --hash=sha256:11387150cad388d62750327a53d3339fad4888b39a6fe233c3afbb54ecffd3aa \
     --hash=sha256:5d108c028108fe2551d1a7b2e8b713341e2cb4fc0aa7dcf966fa4327a5226755
@@ -194,16 +198,12 @@ importlib-resources==6.5.2 \
     # via
     #   -r requirements/requirements.txt
     #   pyelli (pyproject.toml)
-ipython==9.0.2 \
-    --hash=sha256:143ef3ea6fb1e1bffb4c74b114051de653ffb7737a3f7ab1670e657ca6ae8c44 \
-    --hash=sha256:ec7b479e3e5656bf4f58c652c120494df1820f4f28f522fb7ca09e213c2aab52
+ipython==8.34.0 \
+    --hash=sha256:0419883fa46e0baa182c5d50ebb8d6b49df1889fdb70750ad6d8cfe678eda6e3 \
+    --hash=sha256:c31d658e754673ecc6514583e7dda8069e47136eb62458816b7d1e6625948b5a
     # via
     #   pyelli (pyproject.toml)
     #   ipywidgets
-ipython-pygments-lexers==1.1.1 \
-    --hash=sha256:09c0138009e56b6854f9535736f4171d855c8c08a563a0dcd8022f78355c7e81 \
-    --hash=sha256:a9462224a505ade19a605f71f8fa63c2048833ce50abc86768a0d81d876dc81c
-    # via ipython
 ipywidgets==8.1.5 \
     --hash=sha256:3290f526f87ae6e77655555baba4f36681c555b8bdbbff430b70e52c34c86245 \
     --hash=sha256:870e43b1a35656a80c18c9503bbf2d16802db1cb487eec6fab27d683381dde17
@@ -350,10 +350,6 @@ matplotlib-inline==0.1.7 \
     --hash=sha256:8423b23ec666be3d16e16b60bdd8ac4e86e840ebd1dd11a30b9f117f2fa0ab90 \
     --hash=sha256:df192d39a4ff8f21b1895d72e6a13f5fcc5099f00fa84384e0ea28c2cc0653ca
     # via ipython
-narwhals==1.29.1 \
-    --hash=sha256:2f68cfbb2562672c4dfa54f158ed8c2828e9920ef784981cd9114e419c444216 \
-    --hash=sha256:c408acf09e90c116f247cf34f24a3a89d147e3e235b1d3c708cfd1960baf320a
-    # via plotly
 numpy==2.2.3 \
     --hash=sha256:0391ea3622f5c51a2e29708877d56e3d276827ac5447d7f45e9bc4ade8923c52 \
     --hash=sha256:12c045f43b1d2915eca6b880a7f4a256f59d62df4f044788c8ba67709412128d \
@@ -564,9 +560,9 @@ platformdirs==4.3.6 \
     # via
     #   -r requirements/requirements.txt
     #   pint
-plotly==6.0.0 \
-    --hash=sha256:c4aad38b8c3d65e4a5e7dd308b084143b9025c2cc9d5317fc1f1d30958db87d3 \
-    --hash=sha256:f708871c3a9349a68791ff943a5781b1ec04de7769ea69068adcd9202e57653a
+plotly==5.24.1 \
+    --hash=sha256:dbc8ac8339d248a4bcc36e08a5659bacfe1b079390b8953533f4eb22169b4bae \
+    --hash=sha256:f67073a1e637eb0dc3e46324d9d51e2fe76e9727c892dde64ddf1e1b51f29089
     # via pyelli (pyproject.toml)
 prompt-toolkit==3.0.50 \
     --hash=sha256:544748f3860a2623ca5cd6d2795e7a14f3d0e1c3c9728359013f79877fc89bab \
@@ -612,9 +608,7 @@ pure-eval==0.2.3 \
 pygments==2.19.1 \
     --hash=sha256:61c16d2a8576dc0649d9f39e089b5f02bcd27fba10d8fb4dcc28173f7a45151f \
     --hash=sha256:9ea1544ad55cecf4b8242fab6dd35a93bbce657034b0611ee383099054ab6d8c
-    # via
-    #   ipython
-    #   ipython-pygments-lexers
+    # via ipython
 pyparsing==3.2.1 \
     --hash=sha256:506ff4f4386c4cec0590ec19e6302d3aedb992fdc02c761e90416f158dacf8e1 \
     --hash=sha256:61980854fd66de3a90028d679a954d5f2623e83144b5afe5ee86f43d762e5f0a
@@ -848,6 +842,10 @@ stack-data==0.6.3 \
     --hash=sha256:836a778de4fec4dcd1dcd89ed8abff8a221f58308462e1c4aa2a3cf30148f0b9 \
     --hash=sha256:d5558e0c25a4cb0853cddad3d77da9891a08cb85dd9f9f91b9f8cd66e511e695
     # via ipython
+tenacity==9.0.0 \
+    --hash=sha256:807f37ca97d62aa361264d497b0e31e92b8027044942bfa756160d908320d73b \
+    --hash=sha256:93de0c98785b27fcf659856aa9f54bfbd399e29969b0621bc7f762bd441b4539
+    # via plotly
 traitlets==5.14.3 \
     --hash=sha256:9ed0579d3502c94b4b3732ac120375cda96f923114522847de4b3bb98b96b6b7 \
     --hash=sha256:b74e89e397b1ed28cc831db7aea759ba6640cb3de13090ca145426688ff1ac4f
@@ -864,6 +862,7 @@ typing-extensions==4.12.2 \
     #   anywidget
     #   flexcache
     #   flexparser
+    #   ipython
     #   pint
 tzdata==2025.1 \
     --hash=sha256:24894909e88cdb28bd1636c6887801df64cb485bd593f2fd83ef29075a81d694 \

requirements/fitting-requirements.txt

@@ -9,3 +9,8 @@ uv pip compile --extra=fitting --extra=dev --generate-hashes --upgrade\
     --output-file=requirements/dev-requirements.txt \
     requirements/fitting-requirements.txt \
     pyproject.toml
+
+uv pip compile --extra=fitting --extra=dev --extra=docs --generate-hashes --upgrade\
+    --output-file=docs/requirements.txt \
+    requirements/dev-requirements.txt \
+    pyproject.toml