escape-abm 0.0.1__tar.gz

escape_abm-0.0.1/.clang-format

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+BasedOnStyle: LLVM
+IndentWidth: 4
+ColumnLimit: 120
+DerivePointerAlignment: false
+PointerAlignment: Left
+BreakConstructorInitializers: BeforeComma

escape_abm-0.0.1/.cpush.json5

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+{
+    project: "episim37",
+    remotes: {
+        rivanna: "rivanna:episim37",
+        anvil: "anvil:episim37",
+    }
+}

escape_abm-0.0.1/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

escape_abm-0.0.1/LICENSE

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+Copyright (C) 2023 Rector and Visitors of the University of Virginia
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

escape_abm-0.0.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: escape-abm
+Version: 0.0.1
+Summary: Epidemic Simulator Compiler and Programming Environment
+Author-email: Parantapa Bhattacharya <parantapa@virginia.edu>
+Project-URL: Homepage, http://github.com/nssac/escape-abm
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: click
+Requires-Dist: platformdirs
+Requires-Dist: rich
+Requires-Dist: tree-sitter
+Requires-Dist: tree-sitter-esl
+Requires-Dist: jinja2
+Requires-Dist: pygls
+Requires-Dist: platformdirs
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: pandas
+Requires-Dist: pyarrow
+Requires-Dist: polars
+Requires-Dist: h5py
+Requires-Dist: typeguard
+Requires-Dist: pydantic
+
+# ESCAPE: Epidemic Simulator Compiler and Programming Environment
+
+![A man running away from a virus](docs/escape-banner.webp "A man running away from a virus")
+
+The *Epidemic Simulator Compiler and Programming Environment* or ESCAPE
+is a framework for efficiently developing
+high-performance agent based epidemic simulators.
+
+ESCAPE uses a domain specific language
+called the *Epidemic Simulator Language* or ESL,
+which users have to use to define the epidemic simulations.
+The ESL language provides domain specific constructs
+to define compartmental disease models
+and the structure of the contact networks
+on top of which the disease propagate.
+Additionally, ESL also includes general purpose programming constructs
+&mdash; conditionals, loops, functions, variables, etc. &mdash;
+and parallel constructs
+&mdash; select, sample, apply, and reduce &mdash;
+for describing interventions.
+
+ESCAPE provides a compiler that converts
+the epidemic simulators written in ESL into C++ or CUDA programs.
+Simulators created with ESCAPE are high performance
+parallel programs that run on multi-core CPU systems
+or GPU based systems.
+The ESCAPE compiler itself is written in Python.

escape_abm-0.0.1/README.md

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+# ESCAPE: Epidemic Simulator Compiler and Programming Environment
+
+![A man running away from a virus](docs/escape-banner.webp "A man running away from a virus")
+
+The *Epidemic Simulator Compiler and Programming Environment* or ESCAPE
+is a framework for efficiently developing
+high-performance agent based epidemic simulators.
+
+ESCAPE uses a domain specific language
+called the *Epidemic Simulator Language* or ESL,
+which users have to use to define the epidemic simulations.
+The ESL language provides domain specific constructs
+to define compartmental disease models
+and the structure of the contact networks
+on top of which the disease propagate.
+Additionally, ESL also includes general purpose programming constructs
+— conditionals, loops, functions, variables, etc. —
+and parallel constructs
+— select, sample, apply, and reduce —
+for describing interventions.
+
+ESCAPE provides a compiler that converts
+the epidemic simulators written in ESL into C++ or CUDA programs.
+Simulators created with ESCAPE are high performance
+parallel programs that run on multi-core CPU systems
+or GPU based systems.
+The ESCAPE compiler itself is written in Python.

escape_abm-0.0.1/TODO.rst

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+TODOs
+=====
+
+Bugfix
+......
+
+* Upgrade to latest tree-sitter parser
+* Allow negative constants for config and globals
+* Add support to save specific global/config values each tick
+* Add more support for templated identifier and expressions
+
+Base features
+..............
+
+* Support grouped reductions
+* Support codegen for Kokkos / CUDA
+* Support distributed memory implementation using MPI / UPCXX
+
+Performance improvement
+.......................
+
+* Use bitset/succinct datastructure instead of array of bytes
+* Profile cpu code with vtune/advisor
+
+* Merge back to back parallel calls
+* Use differnt / faster random number generator
+

escape_abm-0.0.1/docs/howto-setup-jupyterlab-locally.rst

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+Howto setup Jupyter Lab for local EpiSim37 development
+======================================================
+
+For this setup we shall use the Conda package manager.
+
+Installation instructions for Miniconda can be found
+`here <https://docs.conda.io/en/latest/miniconda.html>`_.
+
+Once setup is done, please ensure that your conda config contains the following:
+
+.. code::
+
+  # ~/.condarc
+
+  channels:
+    - conda-forge
+    - defaults
+  anaconda_upload: false
+  auto_activate_base: false
+
+Create and activate a conda environment.
+
+.. code::
+
+  $ conda create -n episim37 python=3.11 nodejs=20 jupyterlab=4.1.8 gxx_impl_linux-64 cmake ninja hdf5
+  $ conda activate episim37
+
+Install jupyterlab_esl37 (for ESL37 file type support),
+episim37 (for ESL37 language server),
+and jupyterlab-lsp (for allowing Jupyter Lab to use the language server).
+
+
+.. code::
+
+  $ pip install jupyterlab_esl37 episim37 jupyterlab-lsp
+
+Configure jupyterlab-lsp.
+
+.. code::
+
+  # Locate episim37 executable
+  $ which episim37
+  /path/to/miniconda3/envs/episim37/bin/episim37
+
+  # Ensure config directory exits
+  $ mkdir -p $HOME/.jupyter/jupyter_server_config.d
+
+Create the jupyterlab-lsp config file with the following contents:
+
+.. code::
+
+  # $HOME/.jupyter/jupyter_server_config.d/esl37-ls.json
+
+  {
+      "LanguageServerManager": {
+          "language_servers": {
+              "episim37": {
+                  "version": 2,
+                  "argv": [
+                      "/path/to/miniconda3/envs/episim37/bin/episim37",
+                      "language-server",
+                      "io-server"
+                  ],
+                  "languages": [
+                      "esl37"
+                  ],
+                  "mime_types": [
+                      "text/esl37"
+                  ]
+              }
+          }
+      }
+  }
+
+Replace `/path/to/miniconda3/envs/episim37/bin/episim37` with
+the real path of the episim37 executable.
+
+Jupyter Lab should now be configured for opening ESL37 files.
+Start Jupyter Lab using the following command:
+
+.. code::
+
+   $ cd $HOME
+   $ jupyter lab
+
+
+Known Issues
+------------
+
+If your Jupyter kernel keeps crashing on a Apple Mac
+it maybe due to incompatibility with `polars'.
+You can try using the long term release version of polars.
+
+.. code::
+
+   $ pip uninstall polars
+   $ pip install polars-lts-cpu
+

escape_abm-0.0.1/examples/example1.esl

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+# Example 1: In-school NPIs
+
+config enable_hybrid_learning: bool = True
+config enable_day_30_antigen_test: bool = True
+config enable_day_30_pcr_test: bool = False
+config transmissibility_scale: float = 0.3
+
+node
+    pid: int node key
+    is_in_school: bool static
+    home_isolation_start: int
+    home_isolation_end: int
+end
+
+edge
+    target_pid: int target node key
+    source_pid: int source node key
+    duration: int static
+    is_school_edge: bool static
+    is_non_home_edge: bool static
+end
+
+enum c1_state_t
+    S, E, Ipresymp, Isymp, Iasymp, R
+end
+
+contagion c1
+    state type c1_state_t
+
+    transition
+        E -> Ipresymp, p = 0.65, dwell = 3.0
+        E -> Iasymp, p = 0.35, dwell = normal5
+        Ipresymp -> Isymp, dwell = 2.0
+        Isymp -> R, dwell = isymp_r_dwell
+        Iasymp -> R, dwell = normal5
+    end
+
+    transmission
+        Ipresymp => S -> E
+        Isymp => S -> E
+        Iasymp => S -> E
+    end
+
+    susceptibility c1_susceptibility
+    infectivity c1_infectivity
+    transmissibility c1_transmissibility
+    enabled c1_enabled
+end
+
+def c1_susceptibility(v: node) -> float:
+    if v.c1.state == S:
+        return 1.0
+    else:
+        return 0.0
+    end
+end
+
+def c1_infectivity(v: node) -> float:
+    if v.c1.state == Ipresymp:
+        return 0.8
+    elif v.c1.state == Isymp or v.c1.state == Iasymp:
+        return 1.0
+    else:
+        return 0.0
+    end
+end
+
+def c1_transmissibility(e: edge) -> float:
+    return transmissibility_scale * e.duration / 86400
+end
+
+def c1_enabled(e: edge) -> bool:
+    if e.is_non_home_edge and (is_isolating(e.source_node) or is_isolating(e.target_node)):
+        return False
+    elif e.is_school_edge and not is_school_day():
+        return False
+    else:
+        return True
+    end
+end
+
+def is_isolating(n: node) -> bool:
+    if CUR_TICK <= n.home_isolation_start and n.home_isolation_end < CUR_TICK:
+        return True
+    else:
+        return False
+    end
+end
+
+# Sunday = 0, Monday = 1, Tuesday = 2, Wednesday = 3
+# Thursday = 4, Friday = 5
+def is_school_day() -> bool:
+    var day_of_week : int = CUR_TICK % 7
+
+    if enable_hybrid_learning and 1 <= day_of_week and day_of_week <= 3:
+        return True
+    elif 1 <= day_of_week and day_of_week <= 5:
+        return True
+    else:
+        return False
+    end
+end
+
+distribution
+    discrete isymp_r_dwell
+        p = 0.175, v = 1
+        p = 0.175, v = 2
+        p = 0.1, v = 3
+        p = 0.1, v = 4
+        p = 0.1, v = 5
+        p = 0.1, v = 6
+        p = 0.1, v = 7
+        p = 0.05, v = 8
+        p = 0.05, v = 9
+        p = 0.05, v = 10
+    end
+
+    normal normal5
+        mean = 5.0, std = 1.0, min = 0.0
+    end
+end
+
+nodeset susceptibles
+nodeset seed_nodes
+nodeset positive_inschool_nodes
+nodeset will_start_isolation
+
+def intervene():
+    if CUR_TICK < 10:
+        select(susceptibles, [n: node -> bool](n.c1.state == S))
+        sample(seed_nodes, susceptibles, 5, ABSOLUTE)
+        apply(seed_nodes, [n: node]{ n.c1.state = E ; })
+    end
+
+    select(susceptibles, [n: node -> bool](n.c1.state == S))
+
+    if (enable_day_30_antigen_test or enable_day_30_pcr_test) and CUR_TICK >= 30:
+        select(positive_inschool_nodes, [n: node -> bool](
+            (n.c1.state == Ipresymp or n.c1.state == Isymp or n.c1.state == Iasymp)
+            and n.is_in_school
+            and not is_isolating(n)
+        ))
+    end
+
+    if enable_day_30_antigen_test and CUR_TICK >= 30:
+        sample(will_start_isolation, positive_inschool_nodes, 0.8, RELATIVE)
+        apply(will_start_isolation, [n: node]{
+            n.home_isolation_start = CUR_TICK+1
+            n.home_isolation_end = CUR_TICK+15
+        })
+    end
+
+    if enable_day_30_pcr_test and CUR_TICK >= 30:
+        sample(will_start_isolation, positive_inschool_nodes, 0.95, RELATIVE)
+        apply(will_start_isolation, [n: node]{
+            n.home_isolation_start = CUR_TICK+2
+            n.home_isolation_end = CUR_TICK+16
+        })
+    end
+end