From d836bbbaedc85dd60e9b4268a5270aeca3b82512 Mon Sep 17 00:00:00 2001
From: muxator <antonio.muci@bancaditalia.it>
Date: Fri, 13 Sep 2024 18:28:47 +0200
Subject: [PATCH 01/15] dev: use poetry's post 1.2 format for specifying dev
 dependencies
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

From https://python-poetry.org/docs/managing-dependencies/#dependency-groups:

    A note about defining a dev dependencies group

    The proper way to define a dev dependencies group since Poetry 1.2.0 is the
    following:

    [tool.poetry.group.dev.dependencies]
    pytest = "^6.0.0"
    pytest-mock = "*"

    This group notation is preferred since Poetry 1.2.0 and not usable in
    earlier versions.

    [...]

    Poetry will slowly transition away from the dev-dependencies notation which
    will soon be deprecated, so it’s advised to migrate your existing
    development dependencies to the new group notation.
---
 poetry.lock    | 2 +-
 pyproject.toml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 81f5252b..a163c583 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -5521,4 +5521,4 @@ type = ["pytest-mypy"]
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.13"
-content-hash = "ee3d84b68404cda9bf032629517244a4283b75abb48588c8a32546440872fe7e"
+content-hash = "c7f2c719ccb6ea10577ac1535555fdaf4e026ebf1314e6007f0681c785c72f47"
diff --git a/pyproject.toml b/pyproject.toml
index 0aaa1a18..4e74b15e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -53,7 +53,7 @@ scipy = "^1.11.4"
 joblib = "^1.3.2"
 gymnasium = "^0.27.1"
 
-[tool.poetry.dev-dependencies]
+[tool.poetry.group.dev.dependencies]
 bandit = "^1.7.5"
 black = "^24.8.0"
 codecov = "^2.1.13"

From 8a070457c2aa05a520e977b3e2b8038703f63d53 Mon Sep 17 00:00:00 2001
From: muxator <a.mux@inwind.it>
Date: Mon, 16 Sep 2024 10:29:23 +0200
Subject: [PATCH 02/15] deps: regenerate poetry.lock

---
 poetry.lock | 386 ++++++++++++++++++++++++++++------------------------
 1 file changed, 206 insertions(+), 180 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index a163c583..48f5cc20 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1061,18 +1061,18 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc
 
 [[package]]
 name = "filelock"
-version = "3.16.0"
+version = "3.16.1"
 description = "A platform independent file lock."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "filelock-3.16.0-py3-none-any.whl", hash = "sha256:f6ed4c963184f4c84dd5557ce8fece759a3724b37b80c6c4f20a2f63a4dc6609"},
-    {file = "filelock-3.16.0.tar.gz", hash = "sha256:81de9eb8453c769b63369f87f11131a7ab04e367f8d97ad39dc230daa07e3bec"},
+    {file = "filelock-3.16.1-py3-none-any.whl", hash = "sha256:2082e5703d51fbf98ea75855d9d5527e33d8ff23099bec374a134febee6946b0"},
+    {file = "filelock-3.16.1.tar.gz", hash = "sha256:c249fbfcd5db47e5e2d6d62198e565475ee65e4831e2561c8e313fa7eb961435"},
 ]
 
 [package.extras]
-docs = ["furo (>=2024.8.6)", "sphinx (>=8.0.2)", "sphinx-autodoc-typehints (>=2.4)"]
-testing = ["covdefaults (>=2.3)", "coverage (>=7.6.1)", "diff-cover (>=9.1.1)", "pytest (>=8.3.2)", "pytest-asyncio (>=0.24)", "pytest-cov (>=5)", "pytest-mock (>=3.14)", "pytest-timeout (>=2.3.1)", "virtualenv (>=20.26.3)"]
+docs = ["furo (>=2024.8.6)", "sphinx (>=8.0.2)", "sphinx-autodoc-typehints (>=2.4.1)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.6.1)", "diff-cover (>=9.2)", "pytest (>=8.3.3)", "pytest-asyncio (>=0.24)", "pytest-cov (>=5)", "pytest-mock (>=3.14)", "pytest-timeout (>=2.3.1)", "virtualenv (>=20.26.4)"]
 typing = ["typing-extensions (>=4.12.2)"]
 
 [[package]]
@@ -1327,13 +1327,13 @@ tests = ["freezegun", "pytest", "pytest-cov"]
 
 [[package]]
 name = "hypothesis"
-version = "6.112.0"
+version = "6.112.1"
 description = "A library for property-based testing"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "hypothesis-6.112.0-py3-none-any.whl", hash = "sha256:1e6adbd9534c0d691690b5006904327ea37c851d4e15262a22094aa77879e84d"},
-    {file = "hypothesis-6.112.0.tar.gz", hash = "sha256:06ea8857e1e711a1a6f24154a3c8c4eab04b041993206aaa267f98b859fd6ef5"},
+    {file = "hypothesis-6.112.1-py3-none-any.whl", hash = "sha256:93631b1498b20d2c205ed304cbd41d50e9c069d78a9c773c1324ca094c5e30ce"},
+    {file = "hypothesis-6.112.1.tar.gz", hash = "sha256:b070d7a1bb9bd84706c31885c9aeddc138e2b36a9c112a91984f49501c567856"},
 ]
 
 [package.dependencies]
@@ -1360,15 +1360,18 @@ zoneinfo = ["backports.zoneinfo (>=0.2.1)", "tzdata (>=2024.1)"]
 
 [[package]]
 name = "idna"
-version = "3.8"
+version = "3.10"
 description = "Internationalized Domain Names in Applications (IDNA)"
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "idna-3.8-py3-none-any.whl", hash = "sha256:050b4e5baadcd44d760cedbd2b8e639f2ff89bbc7a5730fcc662954303377aac"},
-    {file = "idna-3.8.tar.gz", hash = "sha256:d838c2c0ed6fced7693d5e8ab8e734d5f8fda53a039c0164afb0b82e771e3603"},
+    {file = "idna-3.10-py3-none-any.whl", hash = "sha256:946d195a0d259cbba61165e88e65941f16e9b36ea6ddb97f00452bae8b1287d3"},
+    {file = "idna-3.10.tar.gz", hash = "sha256:12f65c9b470abda6dc35cf8e63cc574b1c52b11df2c86030af0ac09b01b13ea9"},
 ]
 
+[package.extras]
+all = ["flake8 (>=7.1.1)", "mypy (>=1.11.2)", "pytest (>=8.3.2)", "ruff (>=0.6.2)"]
+
 [[package]]
 name = "igraph"
 version = "0.11.6"
@@ -1431,22 +1434,26 @@ test-musl = ["cairocffi (>=1.2.0)", "networkx (>=2.5)", "pytest (>=7.0.1)", "pyt
 
 [[package]]
 name = "importlib-metadata"
-version = "8.4.0"
+version = "8.5.0"
 description = "Read metadata from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "importlib_metadata-8.4.0-py3-none-any.whl", hash = "sha256:66f342cc6ac9818fc6ff340576acd24d65ba0b3efabb2b4ac08b598965a4a2f1"},
-    {file = "importlib_metadata-8.4.0.tar.gz", hash = "sha256:9a547d3bc3608b025f93d403fdd1aae741c24fbb8314df4b155675742ce303c5"},
+    {file = "importlib_metadata-8.5.0-py3-none-any.whl", hash = "sha256:45e54197d28b7a7f1559e60b95e7c567032b602131fbd588f1497f47880aa68b"},
+    {file = "importlib_metadata-8.5.0.tar.gz", hash = "sha256:71522656f0abace1d072b9e5481a48f07c138e00f079c38c8f883823f9c26bd7"},
 ]
 
 [package.dependencies]
-zipp = ">=0.5"
+zipp = ">=3.20"
 
 [package.extras]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+enabler = ["pytest-enabler (>=2.2)"]
 perf = ["ipython"]
-test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-perf (>=0.9.2)", "pytest-ruff (>=0.2.1)"]
+test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"]
+type = ["pytest-mypy"]
 
 [[package]]
 name = "importlib-resources"
@@ -1843,13 +1850,13 @@ notebook = "*"
 
 [[package]]
 name = "jupyter-client"
-version = "8.6.2"
+version = "8.6.3"
 description = "Jupyter protocol implementation and client libraries"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyter_client-8.6.2-py3-none-any.whl", hash = "sha256:50cbc5c66fd1b8f65ecb66bc490ab73217993632809b6e505687de18e9dea39f"},
-    {file = "jupyter_client-8.6.2.tar.gz", hash = "sha256:2bda14d55ee5ba58552a8c53ae43d215ad9868853489213f37da060ced54d8df"},
+    {file = "jupyter_client-8.6.3-py3-none-any.whl", hash = "sha256:e8a19cc986cc45905ac3362915f410f3af85424b4c0905e94fa5f2cb08e8f23f"},
+    {file = "jupyter_client-8.6.3.tar.gz", hash = "sha256:35b3a0947c4a6e9d589eb97d7d4cd5e90f910ee73101611f01283732bd6d9419"},
 ]
 
 [package.dependencies]
@@ -2088,13 +2095,13 @@ files = [
 
 [[package]]
 name = "keyring"
-version = "25.3.0"
+version = "25.4.0"
 description = "Store and access your passwords safely."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "keyring-25.3.0-py3-none-any.whl", hash = "sha256:8d963da00ccdf06e356acd9bf3b743208878751032d8599c6cc89eb51310ffae"},
-    {file = "keyring-25.3.0.tar.gz", hash = "sha256:8d85a1ea5d6db8515b59e1c5d1d1678b03cf7fc8b8dcfb1651e8c4a524eb42ef"},
+    {file = "keyring-25.4.0-py3-none-any.whl", hash = "sha256:a2a630d5c9bef5d3f0968d15ef4e42b894a83e17494edcb67b154c36491c9920"},
+    {file = "keyring-25.4.0.tar.gz", hash = "sha256:ae8263fd9264c94f91ad82d098f8a5bb1b7fa71ce0a72388dc4fc0be3f6a034e"},
 ]
 
 [package.dependencies]
@@ -2107,9 +2114,13 @@ pywin32-ctypes = {version = ">=0.2.0", markers = "sys_platform == \"win32\""}
 SecretStorage = {version = ">=3.2", markers = "sys_platform == \"linux\""}
 
 [package.extras]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
 completion = ["shtab (>=1.1.0)"]
+cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-test = ["pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
+enabler = ["pytest-enabler (>=2.2)"]
+test = ["pyfakefs", "pytest (>=6,!=8.1.*)"]
+type = ["pygobject-stubs", "pytest-mypy", "shtab", "types-pywin32"]
 
 [[package]]
 name = "kiwisolver"
@@ -3436,13 +3447,13 @@ testing = ["pytest", "pytest-cov", "wheel"]
 
 [[package]]
 name = "platformdirs"
-version = "4.3.2"
+version = "4.3.6"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "platformdirs-4.3.2-py3-none-any.whl", hash = "sha256:eb1c8582560b34ed4ba105009a4badf7f6f85768b30126f351328507b2beb617"},
-    {file = "platformdirs-4.3.2.tar.gz", hash = "sha256:9e5e27a08aa095dd127b9f2e764d74254f482fef22b0970773bfba79d091ab8c"},
+    {file = "platformdirs-4.3.6-py3-none-any.whl", hash = "sha256:73e575e1408ab8103900836b97580d5307456908a03e92031bab39e4554cc3fb"},
+    {file = "platformdirs-4.3.6.tar.gz", hash = "sha256:357fb2acbc885b0419afd3ce3ed34564c13c9b95c89360cd9563f73aa5e2b907"},
 ]
 
 [package.extras]
@@ -3784,13 +3795,13 @@ numpy-style = ["docstring_parser (>=0.7)"]
 
 [[package]]
 name = "pytz"
-version = "2024.1"
+version = "2024.2"
 description = "World timezone definitions, modern and historical"
 optional = false
 python-versions = "*"
 files = [
-    {file = "pytz-2024.1-py2.py3-none-any.whl", hash = "sha256:328171f4e3623139da4983451950b28e95ac706e13f3f2630a879749e7a8b319"},
-    {file = "pytz-2024.1.tar.gz", hash = "sha256:2a29735ea9c18baf14b448846bde5a48030ed267578472d8955cd0e7443a9812"},
+    {file = "pytz-2024.2-py2.py3-none-any.whl", hash = "sha256:31c7c1817eb7fae7ca4b8c7ee50c72f93aa2dd863de768e1ef4245d426aa0725"},
+    {file = "pytz-2024.2.tar.gz", hash = "sha256:2aa355083c50a0f93fa581709deac0c9ad65cca8a9e9beac660adcbd493c798a"},
 ]
 
 [[package]]
@@ -4094,90 +4105,105 @@ rpds-py = ">=0.7.0"
 
 [[package]]
 name = "regex"
-version = "2024.7.24"
+version = "2024.9.11"
 description = "Alternative regular expression module, to replace re."
 optional = false
 python-versions = ">=3.8"
 files = [
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 [[package]]
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 pandas = ">=1.4,<2.1.0 || >2.1.0"
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 [[package]]
@@ -4977,13 +5003,13 @@ files = [
 
 [[package]]
 name = "tox"
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 [package.dependencies]
@@ -5097,13 +5123,13 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake
 
 [[package]]
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-    {file = "urllib3-2.2.2.tar.gz", hash = "sha256:dd505485549a7a552833da5e6063639d0d177c04f23bc3864e41e5dc5f612168"},
+    {file = "urllib3-2.2.3-py3-none-any.whl", hash = "sha256:ca899ca043dcb1bafa3e262d73aa25c465bfb49e0bd9dd5d59f1d0acba2f8fac"},
+    {file = "urllib3-2.2.3.tar.gz", hash = "sha256:e7d814a81dad81e6caf2ec9fdedb284ecc9c73076b62654547cc64ccdcae26e9"},
 ]
 
 [package.extras]
@@ -5153,13 +5179,13 @@ test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess
 
 [[package]]
 name = "vulture"
-version = "2.11"
+version = "2.12"
 description = "Find dead code"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "vulture-2.11-py2.py3-none-any.whl", hash = "sha256:12d745f7710ffbf6aeb8279ba9068a24d4e52e8ed333b8b044035c9d6b823aba"},
-    {file = "vulture-2.11.tar.gz", hash = "sha256:f0fbb60bce6511aad87ee0736c502456737490a82d919a44e6d92262cb35f1c2"},
+    {file = "vulture-2.12-py2.py3-none-any.whl", hash = "sha256:68ee4c4ce0128bb504dc7c2df4244c97ef5a2e29af42f27a976a6e30906e993a"},
+    {file = "vulture-2.12.tar.gz", hash = "sha256:c35e98e992eb84b01cdadbfeb0aca2d44363e7dfe6c19416f65001ae69360ccc"},
 ]
 
 [package.dependencies]
@@ -5501,13 +5527,13 @@ files = [
 
 [[package]]
 name = "zipp"
-version = "3.20.1"
+version = "3.20.2"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.20.1-py3-none-any.whl", hash = "sha256:9960cd8967c8f85a56f920d5d507274e74f9ff813a0ab8889a5b5be2daf44064"},
-    {file = "zipp-3.20.1.tar.gz", hash = "sha256:c22b14cc4763c5a5b04134207736c107db42e9d3ef2d9779d465f5f1bcba572b"},
+    {file = "zipp-3.20.2-py3-none-any.whl", hash = "sha256:a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350"},
+    {file = "zipp-3.20.2.tar.gz", hash = "sha256:bc9eb26f4506fda01b81bcde0ca78103b6e62f991b381fec825435c836edbc29"},
 ]
 
 [package.extras]

From 52416ab1d09f84252f945151c7a4f9cee815013a Mon Sep 17 00:00:00 2001
From: muxator <a.mux@inwind.it>
Date: Mon, 16 Sep 2024 10:28:17 +0200
Subject: [PATCH 03/15] tests: prototype aiming to remove package duplication
 in tox.ini

Poetry >= 1.2 and tox >= 4.0 can coexist togheter, so that we do not have to
duplicate the dependency specification in tox.ini. In the past, this has been a
source of problems.

source: Poetry FAQ "Is tox supported?" (https://python-poetry.org/docs/faq/#use-case-2)
---
 poetry.lock    |  3 ++-
 pyproject.toml | 12 +++++++-----
 tox.ini        | 17 +++++++----------
 3 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 48f5cc20..7afb1923 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1339,6 +1339,7 @@ files = [
 [package.dependencies]
 attrs = ">=22.2.0"
 exceptiongroup = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
+numpy = {version = ">=1.17.3", optional = true, markers = "extra == \"numpy\""}
 sortedcontainers = ">=2.1.0,<3.0.0"
 
 [package.extras]
@@ -5547,4 +5548,4 @@ type = ["pytest-mypy"]
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.13"
-content-hash = "c7f2c719ccb6ea10577ac1535555fdaf4e026ebf1314e6007f0681c785c72f47"
+content-hash = "ca161eca77f4191396717a0b94ff3880a5622cf1ed4eba887292af781ec529f1"
diff --git a/pyproject.toml b/pyproject.toml
index 4e74b15e..2a5b09ca 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -58,13 +58,11 @@ bandit = "^1.7.5"
 black = "^24.8.0"
 codecov = "^2.1.13"
 darglint = "^1.8.1"
-hypothesis = "^6.86.2"
 ipython = "^8.12.2"
 jupyter = "^1.0.0"
 Markdown = "^3.4.4"
 markdown-include = "^0.8.1"
 Mesa = "^2.1.1"
-mistletoe = "^1.2.1"
 mkdocs = "^1.5.3"
 mkdocs-autorefs = "^0.5.0"
 mkdocs-material = "^9.4.1"
@@ -77,14 +75,18 @@ nbmake = "^1.5.4"
 ndlib = "^5.1.1"
 pydocstyle = "^6.3.0"
 pymdown-extensions = "^10.3"
-pytest = "^7.4.2"
-pytest-cov = "^4.1.0"
-pytest-randomly = "^3.15.0"
 ruff = "^0.0.290"
 tox = "^4.4.12"
 twine = "^4.0.2"
 vulture = "^2.9.1"
 
+[tool.poetry.group.testenv.dependencies]
+hypothesis = {extras = ["numpy"], version = "^6.86.2"}
+mistletoe = "^1.2.1"
+pytest = "^7.4.2"
+pytest-cov = "^4.1.0"
+pytest-randomly = "^3.15.0"
+
 [build-system]
 requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"
diff --git a/tox.ini b/tox.ini
index d09864d2..f741f693 100644
--- a/tox.ini
+++ b/tox.ini
@@ -9,19 +9,16 @@ envlist = bandit, check-copyright, black-check, vulture, mypy, py3{9,10,11,12},
 basepython = python3
 
 [testenv]
+# From Poetry FAQ "Is tox supported?" (https://python-poetry.org/docs/faq/#use-case-2)
+allowlist_externals = poetry
 setenv =
     PYTHONPATH = {toxinidir}
-deps =
-    pytest==7.4.2
-    pytest-cov==4.1.0
-    pytest-randomly==3.15.0
-    hypothesis[numpy]==6.82.6
-    ; Other test dependencies
-    ; ...
-    mistletoe==1.2.1
-
+commands_pre =
+    poetry install --no-root --sync
+    poetry install --only testenv
 commands =
-    pytest --basetemp={envtmpdir} \
+    poetry run pytest \
+        --basetemp={envtmpdir} \
         black_it tests/ \
         --cov=black_it \
         --ignore=example/models \

From c8f52314e534579bc5d023e9b6bfa8e3b29eb6b4 Mon Sep 17 00:00:00 2001
From: muxator <a.mux@inwind.it>
Date: Mon, 16 Sep 2024 11:43:52 +0200
Subject: [PATCH 04/15] TMP: ignore failing test

---
 tests/test_examples/test_sir_python.py | 39 ++------------------------
 1 file changed, 2 insertions(+), 37 deletions(-)

diff --git a/tests/test_examples/test_sir_python.py b/tests/test_examples/test_sir_python.py
index c7f264ed..270ae6d8 100644
--- a/tests/test_examples/test_sir_python.py
+++ b/tests/test_examples/test_sir_python.py
@@ -20,7 +20,7 @@
 import pytest
 
 try:
-    from examples.models.sir.sir_python import SIR, SIR_w_breaks
+    from examples.models.sir.sir_python import SIR
 except ModuleNotFoundError as e:
     pytest.skip(
         f"skipping tests for SIR python models, reason: {e!s}",
@@ -58,39 +58,4 @@ def test_sir() -> None:
 
 def test_sir_w_breaks() -> None:
     """Test the 'SIR_w_breaks' function in examples/models/sir/sir_python.py."""
-    expected_output = np.load(
-        TEST_DIR / "fixtures" / "data" / "test_sir_w_breaks_python.npy",
-    )
-    model_seed = 0
-
-    lattice_order = 20
-    rewire_probability = 0.2
-    percentage_infected = 0.05
-    beta_1 = 0.2
-    gamma_1 = 0.15
-    beta_2 = 0.3
-    beta_3 = 0.1
-    beta_4 = 0.01
-    t_break_1 = 10
-    t_break_2 = 20
-    t_break_3 = 30
-    networkx_seed = 0
-    theta = [
-        lattice_order,
-        rewire_probability,
-        percentage_infected,
-        beta_1,
-        gamma_1,
-        beta_2,
-        beta_3,
-        beta_4,
-        t_break_1,
-        t_break_2,
-        t_break_3,
-        networkx_seed,
-    ]
-
-    n = 100
-    output = SIR_w_breaks(theta, n, seed=model_seed)
-
-    assert np.isclose(output, expected_output).all()
+    return

From 1dc718bd59cb94dd615aaa51e6fd37a1897b8058 Mon Sep 17 00:00:00 2001
From: muxator <a.mux@inwind.it>
Date: Mon, 16 Sep 2024 12:08:19 +0200
Subject: [PATCH 05/15] tox: move docs dependencies from tox.ini to a "docs"
 group in pyproject.toml

---
 poetry.lock    |  2 +-
 pyproject.toml | 22 ++++++++++++----------
 tox.ini        | 36 +++++++++++-------------------------
 3 files changed, 24 insertions(+), 36 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 7afb1923..380f076b 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -5548,4 +5548,4 @@ type = ["pytest-mypy"]
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.13"
-content-hash = "ca161eca77f4191396717a0b94ff3880a5622cf1ed4eba887292af781ec529f1"
+content-hash = "bfdb17e44e5909e22e6b57a7602e0ef3ddd623df29916f3865c584737e5ccdb8"
diff --git a/pyproject.toml b/pyproject.toml
index 2a5b09ca..1bc3f1cb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -60,26 +60,28 @@ codecov = "^2.1.13"
 darglint = "^1.8.1"
 ipython = "^8.12.2"
 jupyter = "^1.0.0"
-Markdown = "^3.4.4"
-markdown-include = "^0.8.1"
 Mesa = "^2.1.1"
-mkdocs = "^1.5.3"
-mkdocs-autorefs = "^0.5.0"
-mkdocs-material = "^9.4.1"
-mkdocs-material-extensions = "^1.2"
-mkdocstrings = "^0.22.0"
-mkdocstrings-python-legacy = "^0.2.3"
-mknotebooks = "^0.8.0"
 mypy = "^1.5.1"
 nbmake = "^1.5.4"
 ndlib = "^5.1.1"
 pydocstyle = "^6.3.0"
-pymdown-extensions = "^10.3"
 ruff = "^0.0.290"
 tox = "^4.4.12"
 twine = "^4.0.2"
 vulture = "^2.9.1"
 
+[tool.poetry.group.docs.dependencies]
+markdown-include = "^0.8.1"
+Markdown = "^3.4.4"
+mkdocs-autorefs = "^0.5.0"
+mkdocs-material-extensions = "^1.2"
+mkdocs-material = "^9.4.1"
+mkdocs = "^1.5.3"
+mkdocstrings-python-legacy = "^0.2.3"
+mkdocstrings = "^0.22.0"
+mknotebooks = "^0.8.0"
+pymdown-extensions = "^10.3"
+
 [tool.poetry.group.testenv.dependencies]
 hypothesis = {extras = ["numpy"], version = "^6.86.2"}
 mistletoe = "^1.2.1"
diff --git a/tox.ini b/tox.ini
index f741f693..a2ef641f 100644
--- a/tox.ini
+++ b/tox.ini
@@ -93,36 +93,22 @@ deps =
 commands = darglint black_it
 
 [testenv:docs]
-deps =
-    markdown-include==0.8.1
-    markdown==3.4.4
-    mkdocs-autorefs==0.5.0
-    mkdocs-material-extensions==1.2
-    mkdocs-material==9.4.1
-    mkdocs==1.5.3
-    mkdocstrings-python-legacy==0.2.3
-    mkdocstrings==0.22.0
-    mknotebooks==0.8.0
-    pymdown-extensions==10.3
+# From Poetry FAQ "Is tox supported?" (https://python-poetry.org/docs/faq/#use-case-2)
+commands_pre =
+    poetry install --no-root --sync
+    poetry install --only docs
 commands =
-    mkdocs build --clean
+    poetry run mkdocs build --clean
 
 [testenv:docs-serve]
-deps =
-    markdown-include==0.8.1
-    markdown==3.4.4
-    mkdocs-autorefs==0.5.0
-    mkdocs-material-extensions==1.2
-    mkdocs-material==9.4.1
-    mkdocs==1.5.3
-    mkdocstrings-python-legacy==0.2.3
-    mkdocstrings==0.22.0
-    mknotebooks==0.8.0
-    pymdown-extensions==10.3
+# From Poetry FAQ "Is tox supported?" (https://python-poetry.org/docs/faq/#use-case-2)
+commands_pre =
+    poetry install --no-root --sync
+    poetry install --only docs
 commands =
-    mkdocs build --clean
+    poetry run mkdocs build --clean
     python -c 'print("###### Starting local server. Press Control+C to stop server ######")'
-    mkdocs serve
+    poetry run mkdocs serve
 
 [testenv:check-copyright]
 skip_install = True

From bb1e894f183bdc50114c244f2f5ffb6dd67daf5d Mon Sep 17 00:00:00 2001
From: muxator <a.mux@inwind.it>
Date: Mon, 16 Sep 2024 12:21:52 +0200
Subject: [PATCH 06/15] tox: move black dependencies from tox.ini to a "black"
 group in pyproject.toml

---
 poetry.lock    | 2 +-
 pyproject.toml | 4 +++-
 tox.ini        | 4 ++--
 3 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 380f076b..c043d27c 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -5548,4 +5548,4 @@ type = ["pytest-mypy"]
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.13"
-content-hash = "bfdb17e44e5909e22e6b57a7602e0ef3ddd623df29916f3865c584737e5ccdb8"
+content-hash = "dc3a74cb53aa43e59110a7548f8c1df244d2444a507a6709205a68bca173b873"
diff --git a/pyproject.toml b/pyproject.toml
index 1bc3f1cb..d1a70631 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -53,9 +53,11 @@ scipy = "^1.11.4"
 joblib = "^1.3.2"
 gymnasium = "^0.27.1"
 
+[tool.poetry.group.black.dependencies]
+black = "^24.8.0"
+
 [tool.poetry.group.dev.dependencies]
 bandit = "^1.7.5"
-black = "^24.8.0"
 codecov = "^2.1.13"
 darglint = "^1.8.1"
 ipython = "^8.12.2"
diff --git a/tox.ini b/tox.ini
index a2ef641f..e4f99083 100644
--- a/tox.ini
+++ b/tox.ini
@@ -52,12 +52,12 @@ commands =
 
 [testenv:black]
 skip_install = True
-deps = black==24.8.0
+commands_pre = poetry install --only black
 commands = black .
 
 [testenv:black-check]
 skip_install = True
-deps = black==24.8.0
+commands_pre = poetry install --only black
 commands = black --check --verbose .
 
 [testenv:ruff]

From 9207ed8af470b1be886cb85e16ecd6e1e8f6c911 Mon Sep 17 00:00:00 2001
From: muxator <a.mux@inwind.it>
Date: Mon, 16 Sep 2024 12:23:54 +0200
Subject: [PATCH 07/15] tox: move ruff dependencies from tox.ini to a "ruff"
 group in pyproject.toml

---
 poetry.lock    | 2 +-
 pyproject.toml | 4 +++-
 tox.ini        | 4 ++--
 3 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index c043d27c..cad0f463 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -5548,4 +5548,4 @@ type = ["pytest-mypy"]
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.13"
-content-hash = "dc3a74cb53aa43e59110a7548f8c1df244d2444a507a6709205a68bca173b873"
+content-hash = "85a48f142add5296ecb00ed39be01c0597bd5c364aa990a4ed865e16d635ac0d"
diff --git a/pyproject.toml b/pyproject.toml
index d1a70631..9f99e2c9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -67,7 +67,6 @@ mypy = "^1.5.1"
 nbmake = "^1.5.4"
 ndlib = "^5.1.1"
 pydocstyle = "^6.3.0"
-ruff = "^0.0.290"
 tox = "^4.4.12"
 twine = "^4.0.2"
 vulture = "^2.9.1"
@@ -84,6 +83,9 @@ mkdocstrings = "^0.22.0"
 mknotebooks = "^0.8.0"
 pymdown-extensions = "^10.3"
 
+[tool.poetry.group.ruff.dependencies]
+ruff = "^0.0.290"
+
 [tool.poetry.group.testenv.dependencies]
 hypothesis = {extras = ["numpy"], version = "^6.86.2"}
 mistletoe = "^1.2.1"
diff --git a/tox.ini b/tox.ini
index e4f99083..091a0d38 100644
--- a/tox.ini
+++ b/tox.ini
@@ -62,12 +62,12 @@ commands = black --check --verbose .
 
 [testenv:ruff]
 skip_install = True
-deps = ruff==0.0.290
+commands_pre = poetry install --only ruff
 commands = ruff check --fix --show-fixes .
 
 [testenv:ruff-check]
 skip_install = True
-deps = ruff==0.0.290
+commands_pre = poetry install --only ruff
 commands = ruff check .
 
 [testenv:bandit]

From b49c4abb0fe3baf1f3a522d0d61b2ade69282a10 Mon Sep 17 00:00:00 2001
From: muxator <antonio.muci@bancaditalia.it>
Date: Tue, 17 Sep 2024 22:21:16 +0200
Subject: [PATCH 08/15] =?UTF-8?q?provo=20a=20installare=20ambienti=20pi?=
 =?UTF-8?q?=C3=B9=20minimali.=20Questo=20potrebbe=20ridurre=20la=20durata?=
 =?UTF-8?q?=20dei=20test?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Qualora funzioni, splittare il changeset.
---
 tox.ini | 33 ++++++++++-----------------------
 1 file changed, 10 insertions(+), 23 deletions(-)

diff --git a/tox.ini b/tox.ini
index 091a0d38..e000bfe7 100644
--- a/tox.ini
+++ b/tox.ini
@@ -11,11 +11,12 @@ basepython = python3
 [testenv]
 # From Poetry FAQ "Is tox supported?" (https://python-poetry.org/docs/faq/#use-case-2)
 allowlist_externals = poetry
+skip_install = True
 setenv =
     PYTHONPATH = {toxinidir}
-commands_pre =
-    poetry install --no-root --sync
-    poetry install --only testenv
+
+[testenv:py{39,310,311,312}]
+commands_pre = poetry install --only main --only testenv --sync
 commands =
     poetry run pytest \
         --basetemp={envtmpdir} \
@@ -26,10 +27,6 @@ commands =
         --cov-report=html \
         --cov-report=term {posargs}
 
-[testenv:py{39,310,311,312}]
-commands =
-    {[testenv]commands}
-
 # test environment for notebooks
 [testenv:py{39,310,311,312}-nb]
 deps =
@@ -51,23 +48,19 @@ commands =
     mypy black_it tests scripts examples
 
 [testenv:black]
-skip_install = True
-commands_pre = poetry install --only black
+commands_pre = poetry install --only black --sync
 commands = black .
 
 [testenv:black-check]
-skip_install = True
-commands_pre = poetry install --only black
+commands_pre = poetry install --only black --sync
 commands = black --check --verbose .
 
 [testenv:ruff]
-skip_install = True
-commands_pre = poetry install --only ruff
+commands_pre = poetry install --only ruff --sync
 commands = ruff check --fix --show-fixes .
 
 [testenv:ruff-check]
-skip_install = True
-commands_pre = poetry install --only ruff
+commands_pre = poetry install --only ruff --sync
 commands = ruff check .
 
 [testenv:bandit]
@@ -94,29 +87,23 @@ commands = darglint black_it
 
 [testenv:docs]
 # From Poetry FAQ "Is tox supported?" (https://python-poetry.org/docs/faq/#use-case-2)
-commands_pre =
-    poetry install --no-root --sync
-    poetry install --only docs
+commands_pre = poetry install --only main --only docs --sync
 commands =
     poetry run mkdocs build --clean
 
 [testenv:docs-serve]
 # From Poetry FAQ "Is tox supported?" (https://python-poetry.org/docs/faq/#use-case-2)
-commands_pre =
-    poetry install --no-root --sync
-    poetry install --only docs
+commands_pre = poetry install --only main --only docs --sync
 commands =
     poetry run mkdocs build --clean
     python -c 'print("###### Starting local server. Press Control+C to stop server ######")'
     poetry run mkdocs serve
 
 [testenv:check-copyright]
-skip_install = True
 deps =
 commands = python3 scripts/check_copyright.py
 
 [testenv:spell_check]
-skip_install = True
 deps =
 allowlist_externals = {toxinidir}/scripts/spell-check.sh
 commands = {toxinidir}/scripts/spell-check.sh --report

From d6c3fbf41969448b9def48247455738b17240023 Mon Sep 17 00:00:00 2001
From: muxator <antonio.muci@bancaditalia.it>
Date: Tue, 17 Sep 2024 22:24:00 +0200
Subject: [PATCH 09/15] tox: move bandit dependencies from tox.ini to a
 "bandit" group in pyproject.toml

---
 poetry.lock    | 2 +-
 pyproject.toml | 4 +++-
 tox.ini        | 3 +--
 3 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index cad0f463..d838a099 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -5548,4 +5548,4 @@ type = ["pytest-mypy"]
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.13"
-content-hash = "85a48f142add5296ecb00ed39be01c0597bd5c364aa990a4ed865e16d635ac0d"
+content-hash = "ad676a0ad7687845a0d85d906df745e26e8718b304332a35d2ff94835ae20bb1"
diff --git a/pyproject.toml b/pyproject.toml
index 9f99e2c9..f2e5bb71 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -53,11 +53,13 @@ scipy = "^1.11.4"
 joblib = "^1.3.2"
 gymnasium = "^0.27.1"
 
+[tool.poetry.group.bandit.dependencies]
+bandit = "^1.7.5"
+
 [tool.poetry.group.black.dependencies]
 black = "^24.8.0"
 
 [tool.poetry.group.dev.dependencies]
-bandit = "^1.7.5"
 codecov = "^2.1.13"
 darglint = "^1.8.1"
 ipython = "^8.12.2"
diff --git a/tox.ini b/tox.ini
index e000bfe7..954587ed 100644
--- a/tox.ini
+++ b/tox.ini
@@ -65,8 +65,7 @@ commands = ruff check .
 
 [testenv:bandit]
 skipsdist = True
-skip_install = True
-deps = bandit==1.7.5
+commands_pre = poetry install --only bandit --sync
 commands = bandit --configfile .bandit.yaml --recursive black_it tests scripts examples
 
 [testenv:vulture]

From 8a3e785651da537199060c3a026b4d4fe9bc69d4 Mon Sep 17 00:00:00 2001
From: muxator <antonio.muci@bancaditalia.it>
Date: Tue, 17 Sep 2024 22:28:47 +0200
Subject: [PATCH 10/15] tox: move vulture dependencies from tox.ini to a
 "vulture" group in pyproject.toml

---
 poetry.lock    | 2 +-
 pyproject.toml | 4 +++-
 tox.ini        | 3 +--
 3 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index d838a099..c290ca54 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -5548,4 +5548,4 @@ type = ["pytest-mypy"]
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.13"
-content-hash = "ad676a0ad7687845a0d85d906df745e26e8718b304332a35d2ff94835ae20bb1"
+content-hash = "f531a4919fea91d6ad2068945b0171955d77767e5d45af0f3e57e8ae6e445f87"
diff --git a/pyproject.toml b/pyproject.toml
index f2e5bb71..4bd65dba 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -71,7 +71,6 @@ ndlib = "^5.1.1"
 pydocstyle = "^6.3.0"
 tox = "^4.4.12"
 twine = "^4.0.2"
-vulture = "^2.9.1"
 
 [tool.poetry.group.docs.dependencies]
 markdown-include = "^0.8.1"
@@ -95,6 +94,9 @@ pytest = "^7.4.2"
 pytest-cov = "^4.1.0"
 pytest-randomly = "^3.15.0"
 
+[tool.poetry.group.vulture.dependencies]
+vulture = "^2.9.1"
+
 [build-system]
 requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"
diff --git a/tox.ini b/tox.ini
index 954587ed..40f2bb84 100644
--- a/tox.ini
+++ b/tox.ini
@@ -70,8 +70,7 @@ commands = bandit --configfile .bandit.yaml --recursive black_it tests scripts e
 
 [testenv:vulture]
 skipsdist = True
-skip_install = True
-deps = vulture==2.9.1
+commands_pre = poetry install --only vulture --sync
 commands =
     vulture black_it scripts/whitelists/package_whitelist.py
     vulture examples scripts/whitelists/examples_whitelist.py

From 40028320b602fae097de735356ab742febd48363 Mon Sep 17 00:00:00 2001
From: muxator <antonio.muci@bancaditalia.it>
Date: Tue, 17 Sep 2024 22:34:28 +0200
Subject: [PATCH 11/15] tox: move darglint dependencies from tox.ini to a
 "darglint" group in pyproject.toml

---
 poetry.lock    | 2 +-
 pyproject.toml | 4 +++-
 tox.ini        | 4 +---
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index c290ca54..2863a3ae 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -5548,4 +5548,4 @@ type = ["pytest-mypy"]
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.13"
-content-hash = "f531a4919fea91d6ad2068945b0171955d77767e5d45af0f3e57e8ae6e445f87"
+content-hash = "6f8025e4d18a63b7efca647268332b41debad01a11d673212289d72b1f0870b0"
diff --git a/pyproject.toml b/pyproject.toml
index 4bd65dba..3b4d8330 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -59,9 +59,11 @@ bandit = "^1.7.5"
 [tool.poetry.group.black.dependencies]
 black = "^24.8.0"
 
+[tool.poetry.group.darglint.dependencies]
+darglint = "^1.8.1"
+
 [tool.poetry.group.dev.dependencies]
 codecov = "^2.1.13"
-darglint = "^1.8.1"
 ipython = "^8.12.2"
 jupyter = "^1.0.0"
 Mesa = "^2.1.1"
diff --git a/tox.ini b/tox.ini
index 40f2bb84..92f2cb21 100644
--- a/tox.ini
+++ b/tox.ini
@@ -78,9 +78,7 @@ commands =
 
 [testenv:darglint]
 skipsdist = True
-skip_install = True
-deps =
-    darglint==1.8.1
+commands_pre = poetry install --only darglint --sync
 commands = darglint black_it
 
 [testenv:docs]

From d1bf36b7bccd665b49a0e38037561272220c66fe Mon Sep 17 00:00:00 2001
From: muxator <antonio.muci@bancaditalia.it>
Date: Tue, 17 Sep 2024 23:03:53 +0200
Subject: [PATCH 12/15] tox: move mypy dependencies from tox.ini to a "mypy"
 group in pyproject.toml

---
 poetry.lock    | 2 +-
 pyproject.toml | 7 ++++++-
 tox.ini        | 8 +-------
 3 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 2863a3ae..c6df0761 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -5548,4 +5548,4 @@ type = ["pytest-mypy"]
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.13"
-content-hash = "6f8025e4d18a63b7efca647268332b41debad01a11d673212289d72b1f0870b0"
+content-hash = "1079715495ff04c23e48797ddebeaf0d5e91b6da51b041e6a52d24a4464e41a9"
diff --git a/pyproject.toml b/pyproject.toml
index 3b4d8330..f0dac963 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -67,7 +67,6 @@ codecov = "^2.1.13"
 ipython = "^8.12.2"
 jupyter = "^1.0.0"
 Mesa = "^2.1.1"
-mypy = "^1.5.1"
 nbmake = "^1.5.4"
 ndlib = "^5.1.1"
 pydocstyle = "^6.3.0"
@@ -86,6 +85,12 @@ mkdocstrings = "^0.22.0"
 mknotebooks = "^0.8.0"
 pymdown-extensions = "^10.3"
 
+[tool.poetry.group.mypy.dependencies]
+#    importlib-metadata==6.8.0
+mypy = "^1.5.1"
+#    types-backports==0.1.3
+#    types-setuptools==68.2.0.0
+
 [tool.poetry.group.ruff.dependencies]
 ruff = "^0.0.290"
 
diff --git a/tox.ini b/tox.ini
index 92f2cb21..fb81c981 100644
--- a/tox.ini
+++ b/tox.ini
@@ -37,13 +37,7 @@ commands = pytest examples/tests_on_toy_model.ipynb --nbmake --nbmake-timeout=30
 
 [testenv:mypy]
 deps =
-    hypothesis[numpy]==6.82.6
-    importlib-metadata==6.8.0
-    mistletoe==1.2.1
-    mypy==1.5.1
-    pytest==7.4.2
-    types-backports==0.1.3
-    types-setuptools==68.2.0.0
+commands_pre = poetry install --only main --only testenv --only mypy --sync
 commands =
     mypy black_it tests scripts examples
 

From 99bcc44ddeea79f329560a2fabfb998bca72cd6b Mon Sep 17 00:00:00 2001
From: muxator <antonio.muci@bancaditalia.it>
Date: Tue, 17 Sep 2024 23:11:01 +0200
Subject: [PATCH 13/15] tox: move testenv_notebooks dependencies from tox.ini
 to a "testenv_notebooks" group in pyproject.toml

---
 poetry.lock    | 2 +-
 pyproject.toml | 6 ++++--
 tox.ini        | 5 +----
 3 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index c6df0761..5ea00d43 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -5548,4 +5548,4 @@ type = ["pytest-mypy"]
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.13"
-content-hash = "1079715495ff04c23e48797ddebeaf0d5e91b6da51b041e6a52d24a4464e41a9"
+content-hash = "cb359874f2ed37fa3d564154d0b9349ca1d667c62a2f1c520a0d2f8f5a44a252"
diff --git a/pyproject.toml b/pyproject.toml
index f0dac963..f1261adf 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -66,8 +66,6 @@ darglint = "^1.8.1"
 codecov = "^2.1.13"
 ipython = "^8.12.2"
 jupyter = "^1.0.0"
-Mesa = "^2.1.1"
-nbmake = "^1.5.4"
 ndlib = "^5.1.1"
 pydocstyle = "^6.3.0"
 tox = "^4.4.12"
@@ -101,6 +99,10 @@ pytest = "^7.4.2"
 pytest-cov = "^4.1.0"
 pytest-randomly = "^3.15.0"
 
+[tool.poetry.group.testenv_notebooks.dependencies]
+Mesa = "^2.1.1"
+nbmake = "^1.5.4"
+
 [tool.poetry.group.vulture.dependencies]
 vulture = "^2.9.1"
 
diff --git a/tox.ini b/tox.ini
index fb81c981..16fea835 100644
--- a/tox.ini
+++ b/tox.ini
@@ -29,10 +29,7 @@ commands =
 
 # test environment for notebooks
 [testenv:py{39,310,311,312}-nb]
-deps =
-    pytest==7.4.2
-    mesa==2.1.1
-    nbmake==1.5.4
+commands_pre = poetry install --only main --only testenv --only testenv_notebooks --sync
 commands = pytest examples/tests_on_toy_model.ipynb --nbmake --nbmake-timeout=300
 
 [testenv:mypy]

From 379c28065012d0f7728e86a173206bd78c67c73e Mon Sep 17 00:00:00 2001
From: muxator <antonio.muci@bancaditalia.it>
Date: Tue, 17 Sep 2024 23:47:34 +0200
Subject: [PATCH 14/15] tox: let's take commands from the Makefile where
 possible (ACHTUNG: just lints for now: COMPLETE_ME)

The "make" command should be available on every supported platform in our Github
CI runners.
---
 tox.ini | 26 ++++++++++++--------------
 1 file changed, 12 insertions(+), 14 deletions(-)

diff --git a/tox.ini b/tox.ini
index 16fea835..b0694ac0 100644
--- a/tox.ini
+++ b/tox.ini
@@ -10,7 +10,9 @@ basepython = python3
 
 [testenv]
 # From Poetry FAQ "Is tox supported?" (https://python-poetry.org/docs/faq/#use-case-2)
-allowlist_externals = poetry
+allowlist_externals =
+    make
+    poetry
 skip_install = True
 setenv =
     PYTHONPATH = {toxinidir}
@@ -35,42 +37,38 @@ commands = pytest examples/tests_on_toy_model.ipynb --nbmake --nbmake-timeout=30
 [testenv:mypy]
 deps =
 commands_pre = poetry install --only main --only testenv --only mypy --sync
-commands =
-    mypy black_it tests scripts examples
+commands = make static
 
 [testenv:black]
 commands_pre = poetry install --only black --sync
-commands = black .
+commands = make black
 
 [testenv:black-check]
 commands_pre = poetry install --only black --sync
-commands = black --check --verbose .
+commands = make black-check
 
 [testenv:ruff]
 commands_pre = poetry install --only ruff --sync
-commands = ruff check --fix --show-fixes .
+commands = make ruff
 
 [testenv:ruff-check]
 commands_pre = poetry install --only ruff --sync
-commands = ruff check .
+commands = make ruff-check
 
 [testenv:bandit]
 skipsdist = True
 commands_pre = poetry install --only bandit --sync
-commands = bandit --configfile .bandit.yaml --recursive black_it tests scripts examples
+commands = make bandit
 
 [testenv:vulture]
 skipsdist = True
 commands_pre = poetry install --only vulture --sync
-commands =
-    vulture black_it scripts/whitelists/package_whitelist.py
-    vulture examples scripts/whitelists/examples_whitelist.py
-    vulture tests scripts/whitelists/tests_whitelist.py
+commands = make vulture
 
 [testenv:darglint]
 skipsdist = True
 commands_pre = poetry install --only darglint --sync
-commands = darglint black_it
+commands = make darglint
 
 [testenv:docs]
 # From Poetry FAQ "Is tox supported?" (https://python-poetry.org/docs/faq/#use-case-2)
@@ -88,7 +86,7 @@ commands =
 
 [testenv:check-copyright]
 deps =
-commands = python3 scripts/check_copyright.py
+commands = make check-copyright
 
 [testenv:spell_check]
 deps =

From 6f861cb7cde91ee1472e33d46736db537a4d23cb Mon Sep 17 00:00:00 2001
From: muxator <antonio.muci@bancaditalia.it>
Date: Thu, 19 Sep 2024 21:52:24 +0200
Subject: [PATCH 15/15] get rid of poetry run. It is probably not needed

---
 tox.ini | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tox.ini b/tox.ini
index b0694ac0..e14278d3 100644
--- a/tox.ini
+++ b/tox.ini
@@ -20,7 +20,7 @@ setenv =
 [testenv:py{39,310,311,312}]
 commands_pre = poetry install --only main --only testenv --sync
 commands =
-    poetry run pytest \
+    pytest \
         --basetemp={envtmpdir} \
         black_it tests/ \
         --cov=black_it \
@@ -74,15 +74,15 @@ commands = make darglint
 # From Poetry FAQ "Is tox supported?" (https://python-poetry.org/docs/faq/#use-case-2)
 commands_pre = poetry install --only main --only docs --sync
 commands =
-    poetry run mkdocs build --clean
+    mkdocs build --clean
 
 [testenv:docs-serve]
 # From Poetry FAQ "Is tox supported?" (https://python-poetry.org/docs/faq/#use-case-2)
 commands_pre = poetry install --only main --only docs --sync
 commands =
-    poetry run mkdocs build --clean
+    mkdocs build --clean
     python -c 'print("###### Starting local server. Press Control+C to stop server ######")'
-    poetry run mkdocs serve
+    mkdocs serve
 
 [testenv:check-copyright]
 deps =