simdec 1.1.0__tar.gz → 1.2.0.dev0__tar.gz

{simdec-1.1.0 → simdec-1.2.0.dev0}/.gitignore

@@ -7,6 +7,9 @@ __pycache__
 .cache/*
 **/.ipynb_checkpoints
 
+# Env variables with direnv
+.envrc
+
 # OS generated files
 .DS_Store*
 
@@ -30,3 +33,4 @@ build/*
 dist/*
 sdist/*
 docs/_build
+app.html

{simdec-1.1.0 → simdec-1.2.0.dev0}/CONTRIBUTING.md

@@ -161,3 +161,39 @@ a release:
 5. Check that release has been deployed to PyPI
 6. Check documentation is built and deployed to readthedocs
 7. Check that auto-generated PR is auto-merged on the conda-forge feedstock repo
+
+## Dashboard
+A live dashboard is available at:
+
+https://simdec.io
+
+The DNS records are available on CPanel and the rest is hosted on Google Cloud
+Platform.
+
+Developing locally requires the installation of GCP CLI and Docker engine.
+
+A few helper commands are provided in the Makefile.
+
+### Local use
+
+The dashboard can be run locally using:
+
+    make serve-dev
+
+If you want to test OAuth, you need to export the following env variables:
+
+    export PANEL_OAUTH_REDIRECT_URI=http://localhost:5006/app
+    export PANEL_OAUTH_KEY=[VALUE IN GCP Secret Manager]
+    export PANEL_OAUTH_SECRET=[VALUE IN GCP Secret Manager]
+    export PANEL_OAUTH_ENCRYPTION=[VALUE IN GCP Secret Manager]
+
+Use the CLI tool `direnv` for convenience. Then you can serve with
+OAuth support:
+
+    make serve-oauth
+
+### Deployment
+
+New version can either be deployed from the CI with `cloudbuild` or locally:
+
+    make production

{simdec-1.1.0 → simdec-1.2.0.dev0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: simdec
-Version: 1.1.0
+Version: 1.2.0.dev0
 Summary: Sensitivity analysis using simulation decomposition
 Project-URL: homepage, https://www.simdec.fi/
 Project-URL: documentation, https://simdec.readthedocs.io
@@ -16,20 +16,28 @@ Classifier: License :: OSI Approved :: BSD License
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Python: >=3.9
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.10
 Requires-Dist: numpy
 Requires-Dist: pandas
-Requires-Dist: panel
 Requires-Dist: salib
 Requires-Dist: seaborn
-Requires-Dist: typer[all]
+Provides-Extra: dashboard
+Requires-Dist: cryptography; extra == 'dashboard'
+Requires-Dist: panel>=1.3.8; extra == 'dashboard'
 Provides-Extra: dev
+Requires-Dist: accessible-pygments; extra == 'dev'
+Requires-Dist: cryptography; extra == 'dev'
 Requires-Dist: hatch; extra == 'dev'
+Requires-Dist: numpydoc; extra == 'dev'
+Requires-Dist: panel>=1.3.8; extra == 'dev'
 Requires-Dist: pre-commit; extra == 'dev'
-Requires-Dist: simdec[doc,test]; extra == 'dev'
+Requires-Dist: pydata-sphinx-theme; extra == 'dev'
+Requires-Dist: pytest; extra == 'dev'
+Requires-Dist: pytest-cov; extra == 'dev'
+Requires-Dist: sphinx; extra == 'dev'
 Provides-Extra: doc
 Requires-Dist: accessible-pygments; extra == 'doc'
 Requires-Dist: numpydoc; extra == 'doc'
@@ -69,30 +77,11 @@ The library is distributed on PyPi and can be installed with:
 
     pip install simdec
 
-To install the development version, download the source and from the root of
-the repository:
-
-    pip install -e .[dev]
-
 ## Dashboard
 A live dashboard is available at:
 
 https://simdec.io
 
-### Local use
-
-The dashboard can be run locally using:
-
-    make serve
-
-### Deployment
-
-The live version of the dashboard is hosted on GCP. To deploy a new version:
-
-    PANEL_TOKEN=... make production
-
-###
-
 ## Citations
 
 The algorithms and visualizations used in this package came primarily out of
@@ -103,13 +92,6 @@ Foundation, and Finnish Foundation for Economic Education.
 If you use SimDec in your research we would appreciate a citation to the
 following publications:
 
-- Kozlova, M., & Yeomans, J. S. (2022). Monte Carlo Enhancement via Simulation
-  Decomposition: A “Must-Have” Inclusion for Many Disciplines. _INFORMS
-  Transactions on Education, 22_(3), 147-159. DOI:10.1287/ited.2019.0240.
-- Kozlova, M., Moss, R. J., Yeomans, J. S., & Caers, J. (forthcoming).
-  Uncovering Heterogeneous Effects in Computational Models for Sustainable
-  Decision-making. _Environmental Modelling & Software_.
-- Kozlova, M., Moss, R. J., Roy, P., Alam, A., & Yeomans, J. S. (forthcoming).
-  SimDec algorithm. In M. Kozlova & J. S. Yeomans (Eds.), _Sensitivity Analysis
-  for Business, Technology, and Policymaking Made Easy with Simulation
-  Decomposition_. Routledge.
+- Kozlova, M., & Yeomans, J. S. (2022). Monte Carlo Enhancement via Simulation Decomposition: A “Must-Have” Inclusion for Many Disciplines. _INFORMS Transactions on Education, 22_(3), 147-159. [Available here](https://pubsonline.informs.org/doi/10.1287/ited.2019.0240).
+- Kozlova, M., Moss, R. J., Yeomans, J. S., & Caers, J. (2024). Uncovering Heterogeneous Effects in Computational Models for Sustainable Decision-making. _Environmental Modelling & Software_, 171, 105898. [https://doi.org/10.1016/j.envsoft.2023.105898](https://doi.org/10.1016/j.envsoft.2023.105898)
+- Kozlova, M., Moss, R. J., Roy, P., Alam, A., & Yeomans, J. S. (forthcoming). SimDec algorithm and guidelines for its usage and interpretation. In M. Kozlova & J. S. Yeomans (Eds.), _Sensitivity Analysis for Business, Technology, and Policymaking. Made Easy with Simulation Decomposition_. Routledge.

{simdec-1.1.0 → simdec-1.2.0.dev0}/README.md

@@ -27,30 +27,11 @@ The library is distributed on PyPi and can be installed with:
 
     pip install simdec
 
-To install the development version, download the source and from the root of
-the repository:
-
-    pip install -e .[dev]
-
 ## Dashboard
 A live dashboard is available at:
 
 https://simdec.io
 
-### Local use
-
-The dashboard can be run locally using:
-
-    make serve
-
-### Deployment
-
-The live version of the dashboard is hosted on GCP. To deploy a new version:
-
-    PANEL_TOKEN=... make production
-
-###
-
 ## Citations
 
 The algorithms and visualizations used in this package came primarily out of
@@ -61,13 +42,6 @@ Foundation, and Finnish Foundation for Economic Education.
 If you use SimDec in your research we would appreciate a citation to the
 following publications:
 
-- Kozlova, M., & Yeomans, J. S. (2022). Monte Carlo Enhancement via Simulation
-  Decomposition: A “Must-Have” Inclusion for Many Disciplines. _INFORMS
-  Transactions on Education, 22_(3), 147-159. DOI:10.1287/ited.2019.0240.
-- Kozlova, M., Moss, R. J., Yeomans, J. S., & Caers, J. (forthcoming).
-  Uncovering Heterogeneous Effects in Computational Models for Sustainable
-  Decision-making. _Environmental Modelling & Software_.
-- Kozlova, M., Moss, R. J., Roy, P., Alam, A., & Yeomans, J. S. (forthcoming).
-  SimDec algorithm. In M. Kozlova & J. S. Yeomans (Eds.), _Sensitivity Analysis
-  for Business, Technology, and Policymaking Made Easy with Simulation
-  Decomposition_. Routledge.
+- Kozlova, M., & Yeomans, J. S. (2022). Monte Carlo Enhancement via Simulation Decomposition: A “Must-Have” Inclusion for Many Disciplines. _INFORMS Transactions on Education, 22_(3), 147-159. [Available here](https://pubsonline.informs.org/doi/10.1287/ited.2019.0240).
+- Kozlova, M., Moss, R. J., Yeomans, J. S., & Caers, J. (2024). Uncovering Heterogeneous Effects in Computational Models for Sustainable Decision-making. _Environmental Modelling & Software_, 171, 105898. [https://doi.org/10.1016/j.envsoft.2023.105898](https://doi.org/10.1016/j.envsoft.2023.105898)
+- Kozlova, M., Moss, R. J., Roy, P., Alam, A., & Yeomans, J. S. (forthcoming). SimDec algorithm and guidelines for its usage and interpretation. In M. Kozlova & J. S. Yeomans (Eds.), _Sensitivity Analysis for Business, Technology, and Policymaking. Made Easy with Simulation Decomposition_. Routledge.

{simdec-1.1.0 → simdec-1.2.0.dev0}/pyproject.toml

@@ -4,10 +4,10 @@ build-backend = "hatchling.build"
 
 [project]
 name = "simdec"
-version = "1.1.0"
+version = "1.2.0dev0"
 description = "Sensitivity analysis using simulation decomposition"
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 license = "BSD-3-Clause"
 authors = [
     { name = "Pamphile Roy" },
@@ -23,9 +23,9 @@ classifiers = [
     "Operating System :: OS Independent",
     "Programming Language :: Python",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
 ]
 
 dependencies = [
@@ -33,11 +33,14 @@ dependencies = [
     "pandas",
     "SALib",
     "seaborn",
-    "typer[all]",
-    "panel",
 ]
 
 [project.optional-dependencies]
+dashboard = [
+    "panel>=1.3.8",
+    "cryptography",
+]
+
 test = [
     "pytest",
     "pytest-cov",
@@ -51,29 +54,33 @@ doc = [
 ]
 
 dev = [
-    "simdec[doc,test]",
+    "simdec[doc,test,dashboard]",
     "pre-commit",
     "hatch",
 ]
 
-[project.scripts]
-simdec = "simdec.workflow:app"
-
 [project.urls]
 homepage = "https://www.simdec.fi/"
 documentation = "https://simdec.readthedocs.io"
 source = "https://github.com/Simulation-Decomposition/simdec-python"
 
 [tool.hatch]
+build.targets.wheel.packages = ["src/simdec"]
 build.targets.sdist.exclude = [
   ".github",
   "docs",
+  "panel",
   "tests",
   "*.rst",
   "*.yml",
   ".*",
+  "Makefile",
+  "Dockerfile",
 ]
 
+[project.entry-points."panel.auth"]
+custom_google = "simdec.auth:CustomGoogleLoginHandler"
+
 [tool.pytest.ini_options]
 addopts = "--durations 10"
 testpaths = [

simdec-1.2.0.dev0/src/simdec/auth.py

@@ -0,0 +1,17 @@
+from panel.auth import GoogleLoginHandler
+from panel.io.resources import CDN_DIST
+
+
+class CustomGoogleLoginHandler(GoogleLoginHandler):
+    def _simple_get(self):
+        html = self._login_template.render(errormessage="", PANEL_CDN=CDN_DIST)
+        self.write(html)
+
+    async def get(self):
+        if "login" in self.request.uri and "state" not in self.request.uri:
+            self._simple_get()
+        else:
+            await super().get()
+
+    async def post(self):
+        await super().get()

{simdec-1.1.0 → simdec-1.2.0.dev0}/src/simdec/decomposition.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 from dataclasses import dataclass
+from hashlib import blake2b
 from typing import Literal
 
 import numpy as np
@@ -14,13 +15,15 @@ __all__ = ["decomposition", "states_expansion"]
 def states_expansion(states: list[int], inputs: pd.DataFrame) -> list[list[str]]:
     """Expand states list to fully represent all scenarios."""
     inputs = pd.DataFrame(inputs)
-    for i, state in enumerate(states):
+    expanded_states = []
+    for state in states:
         if isinstance(state, int):
-            states: list
             if state == 2:
-                states[i] = ["low", "high"]
+                expanded_states.append(["low", "high"])
             elif state == 3:
-                states[i] = ["low", "medium", "high"]
+                expanded_states.append(["low", "medium", "high"])
+        else:
+            expanded_states.append(state)
 
     # categorical for a given variable
     cat_cols = inputs.select_dtypes(exclude=["number"])
@@ -33,9 +36,9 @@ def states_expansion(states: list[int], inputs: pd.DataFrame) -> list[list[str]]
 
     for i, states_cat_ in zip(cat_cols_idx, states_cats_):
         n_unique = np.unique(inputs.iloc[:, i]).size
-        states[i] = list(states_cat_) if n_unique < 5 else states[i]
+        expanded_states[i] = list(states_cat_) if n_unique < 5 else expanded_states[i]
 
-    return states
+    return expanded_states
 
 
 @dataclass
@@ -46,6 +49,17 @@ class DecompositionResult:
     states: list[int]
     bin_edges: np.ndarray
 
+    def __reduce__(self):
+        h = blake2b(key=b"result hashing", digest_size=20)
+
+        h.update(str(self.var_names).encode())
+        h.update(str(self.statistic).encode())
+        h.update(str(self.bins).encode())
+        h.update(str(self.states).encode())
+        h.update(str(self.bin_edges).encode())
+
+        return [h.hexdigest()]
+
 
 def decomposition(
     inputs: pd.DataFrame,
@@ -109,9 +123,13 @@ def decomposition(
 
     # only keep the explained variance corresponding to `dec_limit`
     sensitivity_indices = sensitivity_indices[var_order]
-    n_var_dec = np.where(np.cumsum(sensitivity_indices) < dec_limit)[0].size
-    n_var_dec = max(1, n_var_dec)  # keep at least one variable
-    n_var_dec = min(5, n_var_dec)  # use at most 5 variables
+
+    if auto_ordering:
+        n_var_dec = np.where(np.cumsum(sensitivity_indices) < dec_limit)[0].size
+        n_var_dec = max(1, n_var_dec)  # keep at least one variable
+        n_var_dec = min(5, n_var_dec)  # use at most 5 variables
+    else:
+        n_var_dec = inputs.shape[1]
 
     # 2. states formation
     if states is None:

{simdec-1.1.0 → simdec-1.2.0.dev0}/src/simdec/visualization.py

@@ -1,6 +1,8 @@
+import functools
 import itertools
 from typing import Literal
 
+import colorsys
 import matplotlib as mpl
 import matplotlib.pyplot as plt
 import numpy as np
@@ -11,7 +13,12 @@ from pandas.io.formats.style import Styler
 __all__ = ["visualization", "tableau", "palette"]
 
 
-sequential_palettes = [
+SEQUENTIAL_PALETTES = [
+    "#DC267F",
+    "#E8EA2F",
+    "#26DCD1",
+    "#C552E4",
+    "#3F45D0",
     "Oranges",
     "Purples",
     "Reds",
@@ -33,7 +40,58 @@ sequential_palettes = [
 ]
 
 
-def palette(states: list[int]) -> list[list[float]]:
+@functools.cache
+def sequential_cmaps():
+    cmaps = []
+    for cmap in SEQUENTIAL_PALETTES:
+        try:
+            cmap_ = mpl.colormaps[cmap]
+        except KeyError:
+            color = mpl.colors.hex2color(cmap)
+            cmap_ = single_color_to_colormap(color)
+        cmaps.append(cmap_)
+    return cmaps
+
+
+def single_color_to_colormap(
+    rgba_color: list[float] | str, *, factor: float = 0.5
+) -> mpl.colors.LinearSegmentedColormap:
+    """Create a linear colormap using a single color."""
+    if isinstance(rgba_color, str):
+        rgba_color = mpl.colors.hex2color(rgba_color)
+    # discard alpha channel
+    if len(rgba_color) == 4:
+        *rgb_color, alpha = rgba_color
+    else:
+        alpha = 1.0
+        rgb_color = rgba_color
+        rgba_color = list(rgba_color) + [1]
+
+    # lighten and darken from factor around single color
+    hls_color = colorsys.rgb_to_hls(*rgb_color)
+
+    lightness = hls_color[1]
+    lightened_hls_color = (hls_color[0], lightness * (1 + factor), hls_color[2])
+    lightened_rgb_color = list(colorsys.hls_to_rgb(*lightened_hls_color))
+
+    darkened_hls_color = (hls_color[0], lightness * (1 - factor), hls_color[2])
+    darkened_rgb_color = list(colorsys.hls_to_rgb(*darkened_hls_color))
+
+    lightened_rgba_color = lightened_rgb_color + [alpha]
+    darkened_rgba_color = darkened_rgb_color + [alpha]
+
+    # convert to CMAP
+    cmap = mpl.colors.LinearSegmentedColormap.from_list(
+        "CustomSingleColor",
+        [lightened_rgba_color, rgba_color, darkened_rgba_color],
+        N=3,
+    )
+    return cmap
+
+
+def palette(
+    states: list[int], cmaps: list[mpl.colors.LinearSegmentedColormap] = None
+) -> list[list[float]]:
     """Colour palette.
 
     The product of the states gives the number of scenarios. For each
@@ -43,20 +101,32 @@ def palette(states: list[int]) -> list[list[float]]:
     ----------
     states : list of int
         List of possible states for the considered parameter.
-
+    cmaps : list of LinearSegmentedColormap
+        List of colormaps. Must have the same number of colormaps as the number
+        of first level of states.
     Returns
     -------
-    palette : list of int of size (n, 4)
-        List of colours corresponding to scenarios.
+    palette : list of float of size (n, 4)
+        List of colors corresponding to scenarios. RGBA formatted.
     """
+    n_cmaps = states[0]
+    if cmaps is None:
+        cmaps = sequential_cmaps()[:n_cmaps]
+    else:
+        cmaps = cmaps[:n_cmaps]
+        if len(cmaps) != n_cmaps:
+            raise ValueError(
+                f"Must have the same number of cmaps ({len(cmaps)}) as the "
+                f"number of first states ({n_cmaps})"
+            )
+
     colors = []
     # one palette per first level state, could use more palette when there are
     # many levels
     n_shades = int(np.prod(states[1:]))
-    for i in range(states[0]):
-        palette_ = sequential_palettes[i]
-        cmap = mpl.colormaps[palette_].resampled(n_shades + 1)
-        colors.append(cmap(range(1, n_shades + 1)))
+    for i in range(n_cmaps):
+        cmap = cmaps[i].resampled(n_shades)
+        colors.append(cmap(np.linspace(0, 1, n_shades)))
 
     return np.concatenate(colors).tolist()
 
@@ -108,7 +178,7 @@ def visualization(
     elif kind == "boxplot":
         ax = sns.boxplot(
             bins,
-            palette=palette[::-1],
+            palette=palette,
             orient="h",
             order=list(bins.columns)[::-1],
             ax=ax,
@@ -180,10 +250,10 @@ def tableau(
     # only select/ordering interesting columns
     table = table[["colour", "std", "min", "mean", "max", "probability"]]
 
-    table.insert(loc=0, column="N°", value=np.arange(1, stop=len(table) + 1))
+    table.insert(loc=0, column="N°", value=np.arange(1, stop=len(table) + 1)[::-1])
 
     # style the colour background with palette
-    cmap = mpl.colors.ListedColormap(palette[::-1])
+    cmap = mpl.colors.ListedColormap(palette)
     styler = table.style
     styler.format(precision=2)
     styler.background_gradient(subset=["colour"], cmap=cmap)

simdec-1.1.0/Dockerfile

@@ -1,47 +0,0 @@
-## Step 1/3: Base image
-FROM python:3.11-slim-bookworm as base
-RUN \
-    --mount=type=cache,target=/var/cache/apt \
-    apt-get update && apt-get upgrade -y && apt install curl -y
-
-## Step 2/3: Build/Install app dependencies
-FROM base as builder
-# Allow statements and log messages to immediately appear in the Knative logs
-ENV PYTHONUNBUFFERED True
-
-COPY pyproject.toml README.md /
-
-RUN --mount=type=cache,target=/var/cache/apt apt install -y gcc git
-RUN --mount=type=cache,mode=0777,target=/root/.cache/pip \
-    pip install --upgrade pip setuptools wheel && \
-    pip install -e .  && \
-    mkdir -p /app/src
-
-COPY tests/data /app/tests/data
-COPY src/simdec /app/src/simdec
-COPY app.py /app/app.py
-# matplotlib cache
-RUN mkdir -p /app/.config/matplotlib
-
-# Step 3/3: Image
-FROM  base as panel
-# Allow statements and log messages to immediately appear in the Knative logs
-ENV PYTHONUNBUFFERED True
-ENV PYTHONPATH=/app/src
-ENV PYTHONIOENCODING=utf-8
-ENV ENV=production
-ENV PORT=8080
-
-ARG PANEL_TOKEN
-
-COPY --from=builder /usr/local/lib/python3.11/site-packages/ /usr/local/lib/python3.11/site-packages/
-COPY --from=builder /usr/local/bin/panel /usr/local/bin/panel
-COPY --from=builder /app/src /app/src
-COPY --from=builder /app/tests/data /app/tests/data
-COPY --from=builder /app/app.py /app/app.py
-
-WORKDIR /app
-RUN useradd app && usermod -a -G app app
-USER app
-# Run the web service on container startup.
-CMD panel serve app.py --address 0.0.0.0 --port $PORT --allow-websocket-origin="*" --basic-auth=$PANEL_TOKEN --num-procs 2 --cookie-secret my_super_safe_cookie_secret

simdec-1.1.0/Makefile

@@ -1,95 +0,0 @@
-.PHONY: help prepare doc test serve build publish-production
-.DEFAULT_GOAL := help
-SHELL:=/bin/bash
-
-ifndef version
-   override version = development
-endif
-
-ifndef region
-   override region = europe-north1
-endif
-
-ifndef project
-   override project = delta-entity-401706
-endif
-
-ifndef PANEL_TOKEN
-   # only for local dev, another token is used for deployment
-   override PANEL_TOKEN = e41ea4c145bf13a60c8779c24356
-endif
-
-
-# Add help text after each target name starting with '\#\#'
-help:   ## show this help
-	@echo -e "Help for this makefile\n"
-	@echo "Possible commands are:"
-	@grep -h "##" $(MAKEFILE_LIST) | grep -v grep | sed -e 's/\(.*\):.*##\(.*\)/    \1: \2/'
-
-prepare:  ## Install dependencies and pre-commit hook
-	pip install -e ".[dev]"
-	pre-commit install
-	gcloud init
-	gcloud auth configure-docker
-
-doc:  ## Build Sphinx documentation
-	sphinx-build -b html docs docs/html
-
-test:  ## Run tests with coverage
-	pytest --cov simdec --cov-report term-missing
-
-serve-dev:  ## Serve Panel dashboard - Dev mode
-	panel serve app.py --show --autoreload
-
-serve:  ## Serve Panel dashboard - Prod mode
-	panel serve app.py
-
-build-local:
-	docker build -f ./Dockerfile \
-		--build-arg PANEL_TOKEN=$(PANEL_TOKEN) \
-		--tag simdec-panel:$(version) \
-	    --pull \
-	    ./.
-
-run-local: build-local
-	docker run --rm -it \
-    --name=simdec-panel \
-	--memory=1g \
-	--cpuset-cpus=0 \
-	-e ENV=development \
-	-p "8080:8080" \
-	simdec-panel:$(version)
-
-build:
-	docker build -f ./Dockerfile \
-		--platform linux/amd64 \
-		--build-arg PANEL_TOKEN=$(PANEL_TOKEN) \
-		--tag simdec-panel:$(version) \
-	    --pull \
-	    ./.
-
-run: build
-	docker run --rm -it \
-    --name=simdec-panel \
-	--memory=1g \
-	--cpuset-cpus=0 \
-	-e ENV=development \
-	-p "8080:8080" \
-	simdec-panel:$(version)
-
-publish-production: build
-	docker tag simdec-panel:$(version) $(region)-docker.pkg.dev/$(project)/simdec-panel/simdec-panel:$(version)
-	docker push $(region)-docker.pkg.dev/$(project)/simdec-panel/simdec-panel:$(version)
-
-production: publish-production
-	@echo "Deploying '$(version)'."
-	gcloud run deploy simdec-panel \
-	                  --concurrency=10 \
-	                  --max-instances=1 \
-	                  --region=$(region) \
-	                  --port=8080 \
-	                  --set-env-vars ENV=production \
-	                  --allow-unauthenticated \
-	                  --timeout=600 \
-	                  --image=$(region)-docker.pkg.dev/$(project)/simdec-panel/simdec-panel:$(version) \
-	                  --memory 1Gi

simdec-1.1.0/app.py

@@ -1,358 +0,0 @@
-import bisect
-import io
-
-from bokeh.models import PrintfTickFormatter
-from bokeh.models.widgets.tables import NumberFormatter
-import matplotlib.pyplot as plt
-import numpy as np
-import pandas as pd
-import panel as pn
-
-import simdec as sd
-
-
-# panel app
-pn.extension(template="material")
-pn.extension("tabulator")
-
-pn.config.sizing_mode = "stretch_width"
-pn.config.throttled = True
-font_size = "12pt"
-
-
-@pn.cache
-def load_data(text_fname):
-    if text_fname is None:
-        text_fname = "tests/data/stress.csv"
-    else:
-        text_fname = io.BytesIO(text_fname)
-
-    data = pd.read_csv(text_fname)
-    pn.state.clear_caches()
-    return data
-
-
-@pn.cache
-def column_inputs(data, output):
-    inputs = list(data.columns)
-    inputs.remove(output)
-    return inputs
-
-
-@pn.cache
-def filtered_inputs(data, input_names):
-    return data[input_names]
-
-
-@pn.cache
-def column_output(data):
-    return list(data.columns)
-
-
-@pn.cache
-def filtered_output(data, output_name):
-    return data[output_name]
-
-
-@pn.cache
-def sensitivity_indices(inputs, output):
-    sensitivity_indices = sd.sensitivity_indices(inputs=inputs, output=output)
-    if 0.01 < sum(sensitivity_indices.si) < 2.0:
-        indices = sensitivity_indices.si
-    else:
-        indices = sensitivity_indices.first_order
-    return indices
-
-
-def sensitivity_indices_table(si, inputs):
-    var_names = inputs.columns
-    var_order = np.argsort(si)[::-1]
-    var_names = var_names[var_order].tolist()
-
-    si = list(si[var_order])
-    sum_si = sum(si)
-
-    var_names.append("Sum of Indices")
-    si_numerics = si.copy()
-    si.append(0)
-    si_numerics.append(sum_si)
-
-    d = {"Inputs": var_names, "Indices": si, "": si_numerics}
-    df = pd.DataFrame(data=d)
-    formatters = {
-        "Indices": {"type": "progress", "max": sum_si, "color": "#007eff"},
-        "": NumberFormatter(format="0.00"),
-    }
-    widget = pn.widgets.Tabulator(
-        df,
-        show_index=False,
-        formatters=formatters,
-        theme="bulma",
-    )
-    widget.style.apply(
-        lambda x: ["font-style: italic"] * 3, axis=1, subset=df.index[-1]
-    )
-    widget.style.apply(lambda x: ["font-size: 11pt"] * len(si))
-    return widget
-
-
-@pn.cache
-def explained_variance(si):
-    return sum(si) + np.finfo(np.float64).eps
-
-
-def filtered_si(sensitivity_indices_table, input_names):
-    df = sensitivity_indices_table.value
-    si = []
-    for input_name in input_names:
-        si.append(df.loc[df["Inputs"] == input_name, "Indices"])
-    return np.asarray(si).flatten()
-
-
-def explained_variance_80(sensitivity_indices_table):
-    si = sensitivity_indices_table.value["Indices"]
-    pos_80 = bisect.bisect_right(np.cumsum(si), 0.8)
-
-    # pos_80 = max(2, pos_80)
-    # pos_80 = min(len(si), pos_80)
-
-    input_names = sensitivity_indices_table.value["Inputs"]
-    return input_names.to_list()[: pos_80 + 1]
-
-
-def decomposition(dec_limit, si, inputs, output):
-    return sd.decomposition(
-        inputs=inputs,
-        output=output,
-        sensitivity_indices=si,
-        dec_limit=dec_limit,
-        auto_ordering=False,
-    )
-
-
-def palette(res):
-    return sd.palette(res.states)
-
-
-def n_bins_auto(res):
-    min_ = np.nanmin(res.bins)
-    max_ = np.nanmax(res.bins)
-    return len(np.histogram_bin_edges(res.bins, bins="auto", range=(min_, max_))) - 1
-
-
-def display_n_bins(kind):
-    if kind != "Stacked histogram":
-        return
-
-    return selector_n_bins
-
-
-def figure(res, palette, n_bins, kind, output_name):
-    kind = "histogram" if kind == "Stacked histogram" else "boxplot"
-    plt.close("all")
-    fig, ax = plt.subplots()
-    _ = sd.visualization(
-        bins=res.bins, palette=palette, n_bins=n_bins, kind=kind, ax=ax
-    )
-    ax.set(xlabel=output_name)
-    return fig
-
-
-def states_from_data(res, inputs):
-    return sd.states_expansion(states=res.states, inputs=inputs)
-
-
-def tableau(res, states, palette):
-    # use a notebook to see the styling
-    _, styler = sd.tableau(
-        statistic=res.statistic,
-        var_names=res.var_names,
-        states=states,
-        bins=res.bins,
-        palette=palette,
-    )
-    return styler
-
-
-def tableau_states(res, states):
-    data = []
-    for var_name, states_, bin_edges in zip(res.var_names, states, res.bin_edges):
-        for i, state in enumerate(states_):
-            data.append([var_name, state, bin_edges[i], bin_edges[i + 1]])
-
-    table = pd.DataFrame(data, columns=["variable", "state", "min", "max"])
-    table.set_index(["variable", "state"], inplace=True)
-
-    styler = table.style
-    styler.format(precision=2)
-    styler.set_table_styles([{"selector": "th", "props": [("text-align", "center")]}])
-    return styler
-
-
-# Bindings
-text_fname = pn.widgets.FileInput(sizing_mode="stretch_width", accept=".csv")
-
-interactive_file = pn.bind(load_data, text_fname)
-
-interactive_column_output = pn.bind(column_output, interactive_file)
-selector_output = pn.widgets.Select(name="Output", options=interactive_column_output)
-interactive_output = pn.bind(filtered_output, interactive_file, selector_output)
-
-interactive_column_input = pn.bind(column_inputs, interactive_file, selector_output)
-selector_inputs_sensitivity = pn.widgets.MultiSelect(
-    name="Inputs", value=interactive_column_input, options=interactive_column_input
-)
-interactive_inputs = pn.bind(
-    filtered_output, interactive_file, selector_inputs_sensitivity
-)
-
-interactive_sensitivity_indices = pn.bind(
-    sensitivity_indices, interactive_inputs, interactive_output
-)
-interactive_explained_variance = pn.bind(
-    explained_variance, interactive_sensitivity_indices
-)
-
-interactive_sensitivity_indices_table = pn.bind(
-    sensitivity_indices_table, interactive_sensitivity_indices, interactive_inputs
-)
-
-interactive_explained_variance_80 = pn.bind(
-    explained_variance_80, interactive_sensitivity_indices_table
-)
-selector_inputs_decomposition = pn.widgets.MultiChoice(
-    name="Select inputs for decomposition",
-    value=interactive_explained_variance_80,
-    options=selector_inputs_sensitivity,
-    solid=False,
-)
-interactive_inputs_decomposition = pn.bind(
-    filtered_output, interactive_file, selector_inputs_decomposition
-)
-
-interactive_filtered_si = pn.bind(
-    filtered_si, interactive_sensitivity_indices_table, selector_inputs_decomposition
-)
-interactive_filtered_explained_variance = pn.bind(
-    explained_variance, interactive_filtered_si
-)
-indicator_explained_variance = pn.indicators.Number(
-    name="Explained variance ratio from selected inputs:",
-    value=interactive_filtered_explained_variance,
-    title_size=font_size,
-    font_size=font_size,
-    format="{value:.2f}",
-)
-
-
-interactive_decomposition = pn.bind(
-    decomposition,
-    interactive_explained_variance,
-    interactive_filtered_si,
-    interactive_inputs_decomposition,
-    interactive_output,
-)
-interactive_palette = pn.bind(palette, interactive_decomposition)
-
-switch_histogram_boxplot = pn.widgets.RadioButtonGroup(
-    name="Switch histogram - boxplot",
-    options=["Stacked histogram", "Boxplot"],
-)
-
-interactive_n_bins_auto = pn.bind(n_bins_auto, interactive_decomposition)
-selector_n_bins = pn.widgets.EditableIntSlider(
-    name="Number of bins",
-    start=0,
-    end=100,
-    value=interactive_n_bins_auto,
-    step=10,
-    # bar_color="#FFFFFF",  # does not work
-    format=PrintfTickFormatter(format="%d bins"),
-)
-conditional_selector_n_bins = pn.bind(display_n_bins, switch_histogram_boxplot)
-
-
-interactive_figure = pn.bind(
-    figure,
-    interactive_decomposition,
-    interactive_palette,
-    selector_n_bins,
-    switch_histogram_boxplot,
-    selector_output,
-)
-
-
-interactive_states = pn.bind(
-    states_from_data, interactive_decomposition, interactive_inputs_decomposition
-)
-interactive_tableau = pn.bind(
-    tableau, interactive_decomposition, interactive_states, interactive_palette
-)
-interactive_tableau_states = pn.bind(
-    tableau_states, interactive_decomposition, interactive_states
-)
-
-# App layout
-
-top_description = """
-## Data
-"""
-
-si_description = """
-## Sensitivity Indices
-"""
-
-decomposition_description = """
-## Decomposition
-"""
-
-table_description = """
-## Scenarios
-"""
-
-states_description = """
-## Details on inputs' states
-"""
-
-
-pn_params = pn.layout.WidgetBox(
-    pn.pane.Markdown(top_description, styles={"color": "#0072b5"}),
-    text_fname,
-    selector_output,
-    selector_inputs_sensitivity,
-    pn.pane.Markdown(decomposition_description, styles={"color": "#0072b5"}),
-    selector_inputs_decomposition,
-    indicator_explained_variance,
-    pn.pane.Markdown("## Visualization", styles={"color": "#0072b5"}),
-    switch_histogram_boxplot,
-    conditional_selector_n_bins,
-    max_width=350,
-    sizing_mode="stretch_width",
-).servable(area="sidebar")
-
-pn_app = pn.Column(
-    pn.Row(
-        pn.Column(
-            pn.panel(
-                pn.pane.Matplotlib(
-                    interactive_figure,
-                    tight=True,
-                    format="svg",
-                    sizing_mode="stretch_both",
-                    max_height=500,
-                    height_policy="min",
-                )
-            ),
-            pn.Spacer(height=50),
-            pn.pane.Markdown(si_description, styles={"color": "#0072b5"}),
-            pn.Column(interactive_sensitivity_indices_table, width=400),
-        ),
-        pn.Column(
-            pn.pane.Markdown(table_description, styles={"color": "#0072b5"}),
-            pn.panel(interactive_tableau),
-            pn.Spacer(height=125),
-            pn.pane.Markdown(states_description, styles={"color": "#0072b5"}),
-            pn.panel(interactive_tableau_states),
-        ),
-    )
-).servable(title="Simulation Decomposition Dashboard")