From e8bce3a2646d9d0407eec4ef84e1c9935e961cfa Mon Sep 17 00:00:00 2001 From: "spaceBearAmadeus (Alex)" Date: Tue, 22 Oct 2024 16:08:31 -0400 Subject: [PATCH] updated package version and new documentation --- .../build/doctrees/bio_compose.doctree | Bin 347935 -> 351925 bytes .../build/doctrees/environment.pickle | Bin 120542 -> 121767 bytes .../html/_modules/bio_compose/data_model.html | 17 + .../html/_modules/bio_compose/verifier.html | 8 +- documentation/build/html/bio_compose.html | 36 +- documentation/build/html/genindex.html | 16 +- documentation/build/html/modules.html | 3 +- documentation/build/html/objects.inv | Bin 887 -> 899 bytes documentation/build/html/searchindex.js | 2 +- poetry.lock | 995 +++++++++--------- pyproject.toml | 2 +- 11 files changed, 559 insertions(+), 520 deletions(-) diff --git a/documentation/build/doctrees/bio_compose.doctree b/documentation/build/doctrees/bio_compose.doctree index 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Source code for bio_compose.data_model

         return asdict(self)
+ + +
+[docs] +class DynamicJson: + def __init__(self, data: Dict[Any, Any]): + """ + Dynamically create a JSON-like object from a dictionary/mapping of any shape. + """ + for key, value in data.items(): + if isinstance(value, dict): + value = DynamicData(value) + setattr(self, key, value) + + def __repr__(self): + return f"{self.__dict__}"
+
diff --git a/documentation/build/html/_modules/bio_compose/verifier.html b/documentation/build/html/_modules/bio_compose/verifier.html index 4405c85..95bcfb6 100644 --- a/documentation/build/html/_modules/bio_compose/verifier.html +++ b/documentation/build/html/_modules/bio_compose/verifier.html @@ -392,7 +392,7 @@

Source code for bio_compose.verifier

         n_simulators = len(simulators)
 
         # create subplots
-        fig, axes = plt.subplots(nrows=n_simulators, ncols=1, figsize=(15, 5 * n_simulators))
+        fig, axes = plt.subplots(nrows=n_simulators, ncols=1, figsize=(4, 3 * n_simulators))
 
         # if only one simulator, `axes` won't be an array, so make it an array
         if n_simulators == 1:
@@ -569,9 +569,9 @@ 
Source code for bio_compose.verifier
         self.job_id = self.data.get('content').get('job_id')
         self.verifier = Verifier()
 
-

-[docs]
-    def get_rmse(self, save_dest: str = None, fig_dimensions: tuple[int, int] = None, color_mapping: list[str] = None):
+

+[docs]
+    def get_comparison(self, save_dest: str = None, fig_dimensions: tuple[int, int] = None, color_mapping: list[str] = None):
         """
         Visualize the root-mean-squared error between simulator verification outputs as a heatmap.
 
diff --git a/documentation/build/html/bio_compose.html b/documentation/build/html/bio_compose.html
index cbd585c..abcff3d 100644
--- a/documentation/build/html/bio_compose.html
+++ b/documentation/build/html/bio_compose.html
@@ -68,6 +68,7 @@
 
 
  • bio_compose.data_model
      
 
    • Api
      • 
+
    • DynamicJson
      • 
 
    • RequestError
      • 
 
    • fetch_job()
      • 
 
    • save_plot()
      • 
@@ -412,6 +413,13 @@
 
 
 
+
      
+
      
+class bio_compose.data_model.DynamicJson(data: Dict[Any, Any])[source]
      
+
      Bases: object
      
+
      Dynamically create a JSON-like object from a dictionary/mapping of any shape.
      
+
      
+
 
      
 
      
 class bio_compose.data_model.RequestError(error: str)[source]
      
@@ -600,19 +608,19 @@
 class bio_compose.verifier.VerificationResult(data: dict)[source]
 
      Bases: dict
      
 
      
-
      
-get_output_observables(save_dest: str | None = None, hspace: float = 0.25, use_grid: bool = False)[source]
      
-
      Visualize simulation output (observables) data, not comparison data, with subplots for each species.
      
+
      
+get_comparison(save_dest: str | None = None, fig_dimensions: tuple[int, int] | None = None, color_mapping: list[str] | None = None)[source]
      
+
      Visualize the root-mean-squared error between simulator verification outputs as a heatmap.
      
 
      
 
      Parameters:
      
 
        
-
      • save_dest – (str) path to save the figure. If this value is passed, the figure will be saved in pdf format to this location.
        • 
-
      • hspace – (float) horizontal spacing between subplots. Defaults to 0.25.
        • 
-
      • use_grid – (bool) whether to use a grid for each subplot. Defaults to False.
        • 
+
      • save_dest – (str) destination at which to save figure. Defaults to None.
        • 
+
      • fig_dimensions – (Tuple[int, int], optional) The value to use as the figsize parameter for a call to matplotlib.pyplot.figure(). If None is passed, default to (8, 6).
        • 
+
      • color_mapping – (List[str], optional) list of colors to use for each simulator in the grid. Defaults to None.
        • 
 
      
 
      
 
      Returns:
      
-
      matplotlib Figure and simulation observables indexed by simulator
      
+
      matplotlib Figure and simulator RMSE scores
      
 
      
 
      Return type:
      
 
      Tuple[matplotlib.Figure, Dict]
      
@@ -621,19 +629,19 @@
 
      
 
 
      
-
      
-get_rmse(save_dest: str | None = None, fig_dimensions: tuple[int, int] | None = None, color_mapping: list[str] | None = None)[source]
      
-
      Visualize the root-mean-squared error between simulator verification outputs as a heatmap.
      
+
      
+get_output_observables(save_dest: str | None = None, hspace: float = 0.25, use_grid: bool = False)[source]
      
+
      Visualize simulation output (observables) data, not comparison data, with subplots for each species.
      
 
      
 
      Parameters:
      
 
        
-
      • save_dest – (str) destination at which to save figure. Defaults to None.
        • 
-
      • fig_dimensions – (Tuple[int, int], optional) The value to use as the figsize parameter for a call to matplotlib.pyplot.figure(). If None is passed, default to (8, 6).
        • 
-
      • color_mapping – (List[str], optional) list of colors to use for each simulator in the grid. Defaults to None.
        • 
+
      • save_dest – (str) path to save the figure. If this value is passed, the figure will be saved in pdf format to this location.
        • 
+
      • hspace – (float) horizontal spacing between subplots. Defaults to 0.25.
        • 
+
      • use_grid – (bool) whether to use a grid for each subplot. Defaults to False.
        • 
 
      
 
      
 
      Returns:
      
-
      matplotlib Figure and simulator RMSE scores
      
+
      matplotlib Figure and simulation observables indexed by simulator
      
 
      
 
      Return type:
      
 
      Tuple[matplotlib.Figure, Dict]
      
diff --git a/documentation/build/html/genindex.html b/documentation/build/html/genindex.html
index 6da2d47..611ce88 100644
--- a/documentation/build/html/genindex.html
+++ b/documentation/build/html/genindex.html
@@ -175,6 +175,10 @@ 
      D
      
 
+  
      
   
 
      
@@ -213,15 +217,17 @@ 
      G
      
       
    • generate_port_spec() (bio_compose.bundles.BioBundle method)
 
      • 
       
    • generate_simularium_file() (bio_compose.runner.SimulationRunner method)
+
      • 
+      
    • get_comparison() (bio_compose.verifier.VerificationResult method)
 
      • 
       
    • get_compatible() (bio_compose.verifier.Verifier method)
 
      • 
       
    • get_compatible_verification_simulators() (in module bio_compose.api)
-
      • 
-      
    • get_job_signature() (in module bio_compose.processing_tools)
 
      • 
   
    
   
    • 
       
  • get_output_observables() (bio_compose.verifier.VerificationResult method)
 
    • 
-      
  • get_rmse() (bio_compose.verifier.VerificationResult method)
-
-      
    • 
   
 
 
diff --git a/documentation/build/html/modules.html b/documentation/build/html/modules.html
index 5cad580..b013f32 100644
--- a/documentation/build/html/modules.html
+++ b/documentation/build/html/modules.html
@@ -122,6 +122,7 @@ 
    API DocumentationApi.select_observables()
 
 
+
  • DynamicJson
    • 
 
  • RequestError
      
 
    • RequestError.error
      • 
 
    • RequestError.to_dict()
      • 
@@ -152,8 +153,8 @@ 
      API Documentationbio_compose.verifier
        
 
      • VerificationResult
 
        • 
 
      • Verifier
          
diff --git a/documentation/build/html/objects.inv b/documentation/build/html/objects.inv
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diff --git a/documentation/build/html/searchindex.js b/documentation/build/html/searchindex.js
index baba831..df1163a 100644
--- a/documentation/build/html/searchindex.js
+++ b/documentation/build/html/searchindex.js
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/poetry.lock b/poetry.lock
index b90617a..2f03533 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -79,101 +79,116 @@ files = [
 
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 [[package]]
@@ -288,21 +303,21 @@ tests = ["pytest", "pytest-cov", "pytest-xdist"]
 
 [[package]]
 name = "dnspython"
-version = "2.6.1"
+version = "2.7.0"
 description = "DNS toolkit"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 [package.extras]
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-dnssec = ["cryptography (>=41)"]
+dev = ["black (>=23.1.0)", "coverage (>=7.0)", "flake8 (>=7)", "hypercorn (>=0.16.0)", "mypy (>=1.8)", "pylint (>=3)", "pytest (>=7.4)", "pytest-cov (>=4.1.0)", "quart-trio (>=0.11.0)", "sphinx (>=7.2.0)", "sphinx-rtd-theme (>=2.0.0)", "twine (>=4.0.0)", "wheel (>=0.42.0)"]
+dnssec = ["cryptography (>=43)"]
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-doq = ["aioquic (>=0.9.25)"]
-idna = ["idna (>=3.6)"]
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+idna = ["idna (>=3.7)"]
 trio = ["trio (>=0.23)"]
 wmi = ["wmi (>=1.5.1)"]
 
@@ -333,16 +348,15 @@ test = ["pytest (>=6)"]
 
 [[package]]
 name = "fire"
-version = "0.6.0"
+version = "0.7.0"
 description = "A library for automatically generating command line interfaces."
 optional = false
 python-versions = "*"
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 [package.dependencies]
-six = "*"
 termcolor = "*"
 
 [[package]]
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 [[package]]
@@ -999,95 +1015,90 @@ regex = ">=2022.3.15"
 
 [[package]]
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 description = "Python Imaging Library (Fork)"
 optional = false
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 [package.extras]
-docs = ["furo", "olefile", "sphinx (>=7.3)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinxext-opengraph"]
+docs = ["furo", "olefile", "sphinx (>=8.1)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinxext-opengraph"]
 fpx = ["olefile"]
 mic = ["olefile"]
 tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"]
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 ]
 
 [package.dependencies]
@@ -1253,13 +1264,13 @@ zstd = ["zstandard"]
 
 [[package]]
 name = "pyparsing"
-version = "3.1.4"
+version = "3.2.0"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
 optional = false
-python-versions = ">=3.6.8"
+python-versions = ">=3.9"
 files = [
-    {file = "pyparsing-3.1.4-py3-none-any.whl", hash = "sha256:a6a7ee4235a3f944aa1fa2249307708f893fe5717dc603503c6c7969c070fb7c"},
-    {file = "pyparsing-3.1.4.tar.gz", hash = "sha256:f86ec8d1a83f11977c9a6ea7598e8c27fc5cddfa5b07ea2241edbbde1d7bc032"},
+    {file = "pyparsing-3.2.0-py3-none-any.whl", hash = "sha256:93d9577b88da0bbea8cc8334ee8b918ed014968fd2ec383e868fb8afb1ccef84"},
+    {file = "pyparsing-3.2.0.tar.gz", hash = "sha256:cbf74e27246d595d9a74b186b810f6fbb86726dbf3b9532efb343f6d7294fe9c"},
 ]
 
 [package.extras]
@@ -1495,13 +1506,13 @@ files = [
 
 [[package]]
 name = "sphinx"
-version = "8.0.2"
+version = "8.1.3"
 description = "Python documentation generator"
 optional = false
 python-versions = ">=3.10"
 files = [
-    {file = "sphinx-8.0.2-py3-none-any.whl", hash = "sha256:56173572ae6c1b9a38911786e206a110c9749116745873feae4f9ce88e59391d"},
-    {file = "sphinx-8.0.2.tar.gz", hash = "sha256:0cce1ddcc4fd3532cf1dd283bc7d886758362c5c1de6598696579ce96d8ffa5b"},
+    {file = "sphinx-8.1.3-py3-none-any.whl", hash = "sha256:09719015511837b76bf6e03e42eb7595ac8c2e41eeb9c29c5b755c6b677992a2"},
+    {file = "sphinx-8.1.3.tar.gz", hash = "sha256:43c1911eecb0d3e161ad78611bc905d1ad0e523e4ddc202a58a821773dc4c927"},
 ]
 
 [package.dependencies]
@@ -1515,28 +1526,28 @@ packaging = ">=23.0"
 Pygments = ">=2.17"
 requests = ">=2.30.0"
 snowballstemmer = ">=2.2"
-sphinxcontrib-applehelp = "*"
-sphinxcontrib-devhelp = "*"
-sphinxcontrib-htmlhelp = ">=2.0.0"
-sphinxcontrib-jsmath = "*"
-sphinxcontrib-qthelp = "*"
+sphinxcontrib-applehelp = ">=1.0.7"
+sphinxcontrib-devhelp = ">=1.0.6"
+sphinxcontrib-htmlhelp = ">=2.0.6"
+sphinxcontrib-jsmath = ">=1.0.1"
+sphinxcontrib-qthelp = ">=1.0.6"
 sphinxcontrib-serializinghtml = ">=1.1.9"
 tomli = {version = ">=2", markers = "python_version < \"3.11\""}
 
 [package.extras]
 docs = ["sphinxcontrib-websupport"]
-lint = ["flake8 (>=6.0)", "mypy (==1.11.0)", "pytest (>=6.0)", "ruff (==0.5.5)", "sphinx-lint (>=0.9)", "tomli (>=2)", "types-Pillow (==10.2.0.20240520)", "types-Pygments (==2.18.0.20240506)", "types-colorama (==0.4.15.20240311)", "types-defusedxml (==0.7.0.20240218)", "types-docutils (==0.21.0.20240724)", "types-requests (>=2.30.0)"]
+lint = ["flake8 (>=6.0)", "mypy (==1.11.1)", "pyright (==1.1.384)", "pytest (>=6.0)", "ruff (==0.6.9)", "sphinx-lint (>=0.9)", "tomli (>=2)", "types-Pillow (==10.2.0.20240822)", "types-Pygments (==2.18.0.20240506)", "types-colorama (==0.4.15.20240311)", "types-defusedxml (==0.7.0.20240218)", "types-docutils (==0.21.0.20241005)", "types-requests (==2.32.0.20240914)", "types-urllib3 (==1.26.25.14)"]
 test = ["cython (>=3.0)", "defusedxml (>=0.7.1)", "pytest (>=8.0)", "setuptools (>=70.0)", "typing_extensions (>=4.9)"]
 
 [[package]]
 name = "sphinx-autodoc-typehints"
-version = "2.4.4"
+version = "2.5.0"
 description = "Type hints (PEP 484) support for the Sphinx autodoc extension"
 optional = false
 python-versions = ">=3.10"
 files = [
-    {file = "sphinx_autodoc_typehints-2.4.4-py3-none-any.whl", hash = "sha256:940de2951fd584d147e46772579fdc904f945c5f1ee1a78c614646abfbbef18b"},
-    {file = "sphinx_autodoc_typehints-2.4.4.tar.gz", hash = "sha256:e743512da58b67a06579a1462798a6907664ab77460758a43234adeac350afbf"},
+    {file = "sphinx_autodoc_typehints-2.5.0-py3-none-any.whl", hash = "sha256:53def4753239683835b19bfa8b68c021388bd48a096efcb02cdab508ece27363"},
+    {file = "sphinx_autodoc_typehints-2.5.0.tar.gz", hash = "sha256:259e1026b218d563d72743f417fcc25906a9614897fe37f91bd8d7d58f748c3b"},
 ]
 
 [package.dependencies]
@@ -1643,13 +1654,13 @@ test = ["pytest"]
 
 [[package]]
 name = "termcolor"
-version = "2.4.0"
+version = "2.5.0"
 description = "ANSI color formatting for output in terminal"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "termcolor-2.4.0-py3-none-any.whl", hash = "sha256:9297c0df9c99445c2412e832e882a7884038a25617c60cea2ad69488d4040d63"},
-    {file = "termcolor-2.4.0.tar.gz", hash = "sha256:aab9e56047c8ac41ed798fa36d892a37aca6b3e9159f3e0c24bc64a9b3ac7b7a"},
+    {file = "termcolor-2.5.0-py3-none-any.whl", hash = "sha256:37b17b5fc1e604945c2642c872a3764b5d547a48009871aea3edd3afa180afb8"},
+    {file = "termcolor-2.5.0.tar.gz", hash = "sha256:998d8d27da6d48442e8e1f016119076b690d962507531df4890fcd2db2ef8a6f"},
 ]
 
 [package.extras]
@@ -1668,13 +1679,13 @@ files = [
 
 [[package]]
 name = "tomli"
-version = "2.0.1"
+version = "2.0.2"
 description = "A lil' TOML parser"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
-    {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
+    {file = "tomli-2.0.2-py3-none-any.whl", hash = "sha256:2ebe24485c53d303f690b0ec092806a085f07af5a5aa1464f3931eec36caaa38"},
+    {file = "tomli-2.0.2.tar.gz", hash = "sha256:d46d457a85337051c36524bc5349dd91b1877838e2979ac5ced3e710ed8a60ed"},
 ]
 
 [[package]]
diff --git a/pyproject.toml b/pyproject.toml
index b9ff8b5..7e636af 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,7 +1,7 @@
 # This project configuration should relate only to the high level notebook api (as primary deps).
 [tool.poetry]
 name = "bio-compose"
-version = "0.6.9"
+version = "0.7.0"
 description = "Create, execute, and introspect reproducible composite simulations of dynamic biological systems."
 authors = ["Alex Patrie "]
 readme = "README.md"