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"f6645d316015b48cfe4334b18e7dc5c891b183d3b87753f43e5cd2f77a7bc560" +content-hash = "f577ca4683d5fa565b6138d6f04e21a6ca9a082e3b60a995f6fce1f794b952e8" diff --git a/pyproject.toml b/pyproject.toml index 7b9728250..685ddec5f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "SpectraFit" -version = "1.0.0b2" +version = "0.16.6" description = "Fast fitting of 2D- and 3D-Spectra with established routines" readme = "README.md" authors = ["Anselm Hahn "] @@ -101,7 +101,7 @@ exclude = ["docs/", "tools/"] mkdocs-minify-plugin = "^0.6.2" mkdocs-material = "^9.1.2" jupytext = "^1.14.5" - mkdocs-jupyter = "^0.23.1" + mkdocs-jupyter = "^0.24.0" [build-system] requires = ["poetry-core>=1.0.0"] diff --git a/spectrafit/__init__.py b/spectrafit/__init__.py index 6ad73a32d..8128030bc 100644 --- a/spectrafit/__init__.py +++ b/spectrafit/__init__.py @@ -1,2 +1,2 @@ """SpectraFit, fast command line tool for fitting data.""" -__version__ = "1.0.0b2" +__version__ = "0.16.6" diff --git a/spectrafit/api/report_model.py b/spectrafit/api/report_model.py index d9d4d2692..ac69763f5 100644 --- a/spectrafit/api/report_model.py +++ b/spectrafit/api/report_model.py @@ -47,7 +47,7 @@ class FitMethodAPI(BaseModel): default=False, description="Fitting in the global fashion", ) - confidence_interval: Dict[str, Any] = Field( + confidence_interval: Union[bool, Dict[str, Any]] = Field( ..., description="Settings for the confidence interval calculation", ) diff --git a/spectrafit/plugins/notebook.py b/spectrafit/plugins/notebook.py index 21ba5dd5b..81b3d1252 100644 --- a/spectrafit/plugins/notebook.py +++ b/spectrafit/plugins/notebook.py @@ -569,12 +569,17 @@ def get_linear_correlation(self) -> Dict[str, Any]: return self.args_out["linear_correlation"] @property - def settings_conf_interval(self) -> Dict[str, Any]: + def settings_conf_interval(self) -> Union[bool, Dict[str, Any]]: """Confidence interval settings. Returns: - Dict[str, Any]: Confidence interval settings. + Union[bool, Dict[str, Any]]: Confidence interval settings. """ + if isinstance(self.args_out["conf_interval"], dict): + self.args_out["conf_interval"] = { + key: value if value is not None else {} + for key, value in self.args_out["conf_interval"].items() + } return self.args_out["conf_interval"] @property @@ -582,8 +587,11 @@ def get_confidence_interval(self) -> Dict[Any, Any]: """Get the confidence interval. Returns: - Dict[Any, Any]: Confidence interval as dictionary. + Dict[Any, Any]: Confidence interval as dictionary with or without the + confidence interval results. """ + if self.args_out["conf_interval"] is False: + return {} return self.args_out["confidence_interval"] @property diff --git a/spectrafit/plugins/test/test_notebook.py b/spectrafit/plugins/test/test_notebook.py index 14985470e..c79a45639 100644 --- a/spectrafit/plugins/test/test_notebook.py +++ b/spectrafit/plugins/test/test_notebook.py @@ -571,6 +571,26 @@ def test_conv_2( mock_show.assert_called_once() + def test_conv_no( + self, + class_spectrafit_fit: SpectraFitNotebook, + initial_model: List[Dict[str, Dict[str, Dict[str, Any]]]], + ) -> None: + """Test conf interval via bool for false.""" + sp = class_spectrafit_fit + + with mock.patch(__plotly_io_show__) as mock_show: + sp.solver_model( + initial_model=initial_model, + show_plot=False, + show_df=True, + show_metric=True, + show_peaks=True, + conf_interval=False, + ) + + mock_show.assert_called_once() + def test_display_current_df( self, class_spectrafit_fit: SpectraFitNotebook, From 24a312ca8fd17674a6be9e96afabe0a549abb6de Mon Sep 17 00:00:00 2001 From: Anselm Hahn Date: Mon, 20 Mar 2023 21:59:05 +0100 Subject: [PATCH 2/7] refactor: :arrow_down: Downgrade `mkdocs-jpuyter` to 0.23.1 --- .github/labeler.yml | 4 ++-- poetry.lock | 8 ++++---- pyproject.toml | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/.github/labeler.yml b/.github/labeler.yml index ca2898265..b03844d4b 100644 --- a/.github/labeler.yml +++ b/.github/labeler.yml @@ -20,9 +20,9 @@ pre-commit: - .pre-commit-config.yaml - .pre-commit-hooks.yaml python: - - all: ["./spectrafit/**/*.py", "!./spectrafit/**/test_*.py"] + - any: ["./spectrafit/**/*.py", "!./spectrafit/**/test_*.py"] testing: - - all: ["./spectrafit/**/test_*.py"] + - "./spectrafit/**/test_*.py" docker: - Dockerfile - .dockerignore diff --git a/poetry.lock b/poetry.lock index 446ab2a2a..0fd91b5c1 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2867,14 +2867,14 @@ mkdocs = ">=1.1" [[package]] name = "mkdocs-jupyter" -version = "0.24.0" +version = "0.23.1" description = "Use Jupyter in mkdocs websites" category = "dev" optional = false python-versions = ">=3.7" files = [ - {file = "mkdocs_jupyter-0.24.0-py3-none-any.whl", hash = "sha256:b7ab317d79796c43ac7f15ba8c2bc725b9361011a64300e2b4bb5ba2a73353fa"}, - {file = "mkdocs_jupyter-0.24.0.tar.gz", hash = "sha256:fc2ec9a608609f91080d1fa8183b2ea7e9d2e913dd0e2005979a2c3540fa5cba"}, + {file = "mkdocs_jupyter-0.23.1-py3-none-any.whl", hash = "sha256:0f1f707219af66abb1ead03500fbcb7f7196c6c06d963300ba40b9e8ec8088e8"}, + {file = "mkdocs_jupyter-0.23.1.tar.gz", hash = "sha256:b2745c1e003ef9ec80d43ac8cc00b4de41810a1160bb133eca5329275106ead6"}, ] [package.dependencies] @@ -5933,4 +5933,4 @@ jupyter-dash = ["dash-bootstrap-components", "dash-bootstrap-templates", "ipywid [metadata] lock-version = "2.0" python-versions = ">=3.8,<3.11" -content-hash = "f577ca4683d5fa565b6138d6f04e21a6ca9a082e3b60a995f6fce1f794b952e8" +content-hash = "f6645d316015b48cfe4334b18e7dc5c891b183d3b87753f43e5cd2f77a7bc560" diff --git a/pyproject.toml b/pyproject.toml index 685ddec5f..8ecb517e1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -101,7 +101,7 @@ exclude = ["docs/", "tools/"] mkdocs-minify-plugin = "^0.6.2" mkdocs-material = "^9.1.2" jupytext = "^1.14.5" - mkdocs-jupyter = "^0.24.0" + mkdocs-jupyter = "^0.23.1" [build-system] requires = ["poetry-core>=1.0.0"] From c6e93211e5e0e75ada1271a40ffff25e1aee154c Mon Sep 17 00:00:00 2001 From: Anselm Hahn Date: Mon, 20 Mar 2023 21:59:05 +0100 Subject: [PATCH 3/7] Revert "refactor: :arrow_down: Downgrade `mkdocs-jpuyter` to 0.23.1" This reverts commit 24a312ca8fd17674a6be9e96afabe0a549abb6de. --- .github/labeler.yml | 4 ++-- poetry.lock | 8 ++++---- pyproject.toml | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/.github/labeler.yml b/.github/labeler.yml index b03844d4b..ca2898265 100644 --- a/.github/labeler.yml +++ b/.github/labeler.yml @@ -20,9 +20,9 @@ pre-commit: - .pre-commit-config.yaml - .pre-commit-hooks.yaml python: - - any: ["./spectrafit/**/*.py", "!./spectrafit/**/test_*.py"] + - all: ["./spectrafit/**/*.py", "!./spectrafit/**/test_*.py"] testing: - - "./spectrafit/**/test_*.py" + - all: ["./spectrafit/**/test_*.py"] docker: - Dockerfile - .dockerignore diff --git a/poetry.lock b/poetry.lock index 0fd91b5c1..446ab2a2a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2867,14 +2867,14 @@ mkdocs = ">=1.1" [[package]] name = "mkdocs-jupyter" -version = "0.23.1" +version = "0.24.0" description = "Use Jupyter in mkdocs websites" category = "dev" optional = false python-versions = ">=3.7" files = [ - {file = "mkdocs_jupyter-0.23.1-py3-none-any.whl", hash = "sha256:0f1f707219af66abb1ead03500fbcb7f7196c6c06d963300ba40b9e8ec8088e8"}, - {file = "mkdocs_jupyter-0.23.1.tar.gz", hash = "sha256:b2745c1e003ef9ec80d43ac8cc00b4de41810a1160bb133eca5329275106ead6"}, + {file = "mkdocs_jupyter-0.24.0-py3-none-any.whl", hash = "sha256:b7ab317d79796c43ac7f15ba8c2bc725b9361011a64300e2b4bb5ba2a73353fa"}, + {file = "mkdocs_jupyter-0.24.0.tar.gz", hash = "sha256:fc2ec9a608609f91080d1fa8183b2ea7e9d2e913dd0e2005979a2c3540fa5cba"}, ] [package.dependencies] @@ -5933,4 +5933,4 @@ jupyter-dash = ["dash-bootstrap-components", "dash-bootstrap-templates", "ipywid [metadata] lock-version = "2.0" python-versions = ">=3.8,<3.11" -content-hash = "f6645d316015b48cfe4334b18e7dc5c891b183d3b87753f43e5cd2f77a7bc560" +content-hash = "f577ca4683d5fa565b6138d6f04e21a6ca9a082e3b60a995f6fce1f794b952e8" diff --git a/pyproject.toml b/pyproject.toml index 8ecb517e1..685ddec5f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -101,7 +101,7 @@ exclude = ["docs/", "tools/"] mkdocs-minify-plugin = "^0.6.2" mkdocs-material = "^9.1.2" jupytext = "^1.14.5" - mkdocs-jupyter = "^0.23.1" + mkdocs-jupyter = "^0.24.0" [build-system] requires = ["poetry-core>=1.0.0"] From 7824803a176043b4726b45ff32c1e7c3518a5fec Mon Sep 17 00:00:00 2001 From: Anselm Hahn Date: Mon, 20 Mar 2023 22:06:57 +0100 Subject: [PATCH 4/7] test: :arrow_up: Increase coverage rate --- .github/labeler.yml | 4 ++-- spectrafit/plugins/test/test_notebook.py | 17 +++++++++++++++++ 2 files changed, 19 insertions(+), 2 deletions(-) diff --git a/.github/labeler.yml b/.github/labeler.yml index ca2898265..b03844d4b 100644 --- a/.github/labeler.yml +++ b/.github/labeler.yml @@ -20,9 +20,9 @@ pre-commit: - .pre-commit-config.yaml - .pre-commit-hooks.yaml python: - - all: ["./spectrafit/**/*.py", "!./spectrafit/**/test_*.py"] + - any: ["./spectrafit/**/*.py", "!./spectrafit/**/test_*.py"] testing: - - all: ["./spectrafit/**/test_*.py"] + - "./spectrafit/**/test_*.py" docker: - Dockerfile - .dockerignore diff --git a/spectrafit/plugins/test/test_notebook.py b/spectrafit/plugins/test/test_notebook.py index c79a45639..b35be84ac 100644 --- a/spectrafit/plugins/test/test_notebook.py +++ b/spectrafit/plugins/test/test_notebook.py @@ -603,3 +603,20 @@ def test_display_current_df( sp.display_original_df() sp.display_preprocessed_df() sp.display_fit_df() + + def test_confidence_interval_false_expot( + self, + class_spectrafit_fit: SpectraFitNotebook, + initial_model: List[Dict[str, Dict[str, Dict[str, Any]]]], + ) -> None: + """Test the confidence interval function.""" + sp = class_spectrafit_fit + sp.solver_model( + initial_model=initial_model, + show_plot=False, + show_df=False, + show_metric=False, + show_peaks=False, + conf_interval=False, + ) + sp.generate_report From 6750616069ffb48565889026e53e292740629db9 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 22 Mar 2023 06:18:30 +0000 Subject: [PATCH 5/7] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- poetry.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/poetry.lock b/poetry.lock index 2f21a0448..4189d8c40 100644 --- a/poetry.lock +++ b/poetry.lock @@ -5932,4 +5932,4 @@ jupyter-dash = ["jupyter-dash", "ipywidgets", "dash-bootstrap-components", "dash [metadata] lock-version = "2.0" python-versions = ">=3.8,<3.11" -content-hash = "f577ca4683d5fa565b6138d6f04e21a6ca9a082e3b60a995f6fce1f794b952e8" \ No newline at end of file +content-hash = "f577ca4683d5fa565b6138d6f04e21a6ca9a082e3b60a995f6fce1f794b952e8" From b6553ae145be2e53887c4fc4c17d73ebcf6f5545 Mon Sep 17 00:00:00 2001 From: Anselm Hahn Date: Wed, 22 Mar 2023 07:19:00 +0100 Subject: [PATCH 6/7] build: :pushpin: Update versions in `lock` --- poetry.lock | 27 ++++++++++++++------------- 1 file changed, 14 insertions(+), 13 deletions(-) diff --git a/poetry.lock b/poetry.lock index 4189d8c40..f00838ed7 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry and should not be changed by hand. +# This file is automatically @generated by Poetry 1.4.1 and should not be changed by hand. [[package]] name = "aiofiles" @@ -2114,14 +2114,14 @@ test = ["codecov", "ipykernel", "jupyterlab-server[openapi]", "openapi-spec-vali [[package]] name = "jupyterlab-widgets" -version = "3.0.5" +version = "3.0.6" description = "Jupyter interactive widgets for JupyterLab" category = "main" optional = true python-versions = ">=3.7" files = [ - {file = "jupyterlab_widgets-3.0.5-py3-none-any.whl", hash = "sha256:a04a42e50231b355b7087e16a818f541e53589f7647144ea0344c4bf16f300e5"}, - {file = "jupyterlab_widgets-3.0.5.tar.gz", hash = "sha256:eeaecdeaf6c03afc960ddae201ced88d5979b4ca9c3891bcb8f6631af705f5ef"}, + {file = "jupyterlab_widgets-3.0.6-py3-none-any.whl", hash = "sha256:e95d08adf4f9c37a57da5fff8a65d00480199885fd2ecd2583fd9560b594b4e9"}, + {file = "jupyterlab_widgets-3.0.6.tar.gz", hash = "sha256:a464d68a7b9ebabdc135196389381412a39503d89302be0867d0ff3b2428ebb8"}, ] [[package]] @@ -5041,7 +5041,7 @@ numpy = {version = ">=1.17", markers = "python_version != \"3.10\" or platform_s packaging = ">=21.3" pandas = ">=0.25" patsy = ">=0.5.2" -scipy = {version = ">=1.3", markers = "(python_version > \"3.7\" or platform_system != \"Windows\" or platform_machine != \"x86\") and python_version < \"3.12\""} +scipy = {version = ">=1.3", markers = "python_version > \"3.7\" and python_version < \"3.12\" or platform_system != \"Windows\" and python_version < \"3.12\" or platform_machine != \"x86\" and python_version < \"3.12\""} [package.extras] build = ["cython (>=0.29.32)"] @@ -5091,7 +5091,7 @@ numpy = [ packaging = ">=21.3" pandas = ">=0.25" patsy = ">=0.5.2" -scipy = {version = ">=1.3", markers = "(python_version > \"3.9\" or platform_system != \"Windows\" or platform_machine != \"x86\") and python_version < \"3.12\""} +scipy = {version = ">=1.3", markers = "python_version > \"3.9\" and python_version < \"3.12\" or platform_system != \"Windows\" and python_version < \"3.12\" or platform_machine != \"x86\" and python_version < \"3.12\""} [package.extras] build = ["cython (>=0.29.32)"] @@ -5659,14 +5659,14 @@ watchdog = ["watchdog"] [[package]] name = "widgetsnbextension" -version = "4.0.5" +version = "4.0.6" description = "Jupyter interactive widgets for Jupyter Notebook" category = "main" optional = true python-versions = ">=3.7" files = [ - {file = "widgetsnbextension-4.0.5-py3-none-any.whl", hash = "sha256:eaaaf434fb9b08bd197b2a14ffe45ddb5ac3897593d43c69287091e5f3147bf7"}, - {file = "widgetsnbextension-4.0.5.tar.gz", hash = "sha256:003f716d930d385be3fd9de42dd9bf008e30053f73bddde235d14fbeaeff19af"}, + {file = "widgetsnbextension-4.0.6-py3-none-any.whl", hash = "sha256:7df2bffa274b0b416c1fa0789e321451858a9e276e1220b40a16cc994192e2b7"}, + {file = "widgetsnbextension-4.0.6.tar.gz", hash = "sha256:1a07d06c881a7c16ca7ab4541b476edbe2e404f5c5f0cf524ffa2406a8bd7c80"}, ] [[package]] @@ -5924,12 +5924,13 @@ docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] [extras] -all = ["jupyterlab", "plotly", "itables", "kaleido", "dtale", "networkx", "pydot", "jupyter-dash", "ipywidgets", "dash-bootstrap-components", "dash-bootstrap-templates"] +all = ["dash-bootstrap-components", "dash-bootstrap-templates", "dtale", "ipywidgets", "itables", "jupyter-dash", "jupyterlab", "kaleido", "networkx", "plotly", "pydot"] graph = ["networkx", "pydot"] -jupyter = ["jupyterlab", "plotly", "itables", "kaleido", "dtale"] -jupyter-dash = ["jupyter-dash", "ipywidgets", "dash-bootstrap-components", "dash-bootstrap-templates"] +jupyter = ["dtale", "itables", "jupyterlab", "kaleido", "plotly"] +jupyter-dash = ["dash-bootstrap-components", "dash-bootstrap-templates", "ipywidgets", "jupyter-dash"] [metadata] lock-version = "2.0" -python-versions = ">=3.8,<3.11" + python-versions = ">=3.8,<3.11" content-hash = "f577ca4683d5fa565b6138d6f04e21a6ca9a082e3b60a995f6fce1f794b952e8" + From 91af2cd0edfc216f8440d8b433658ba2ba445ae6 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 22 Mar 2023 06:20:55 +0000 Subject: [PATCH 7/7] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- poetry.lock | 1 - 1 file changed, 1 deletion(-) diff --git a/poetry.lock b/poetry.lock index f00838ed7..89399ef7d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -5933,4 +5933,3 @@ jupyter-dash = ["dash-bootstrap-components", "dash-bootstrap-templates", "ipywid lock-version = "2.0" python-versions = ">=3.8,<3.11" content-hash = "f577ca4683d5fa565b6138d6f04e21a6ca9a082e3b60a995f6fce1f794b952e8" -