[med-svn] [Git][med-team/python-epimodels][master] 5 commits: routine-update: Fix watchfile to detect new versions on github

Steffen Möller (@moeller) gitlab at salsa.debian.org
Fri Sep 3 15:16:51 BST 2021



Steffen Möller pushed to branch master at Debian Med / python-epimodels


Commits:
4fcb8e5b by Steffen Moeller at 2021-09-03T16:06:46+02:00
routine-update: Fix watchfile to detect new versions on github

- - - - -
f4d63746 by Steffen Moeller at 2021-09-03T16:06:49+02:00
routine-update: New upstream version

- - - - -
be5db31b by Steffen Moeller at 2021-09-03T16:06:50+02:00
New upstream version 0.3.20
- - - - -
90bc6326 by Steffen Moeller at 2021-09-03T16:06:51+02:00
Update upstream source from tag 'upstream/0.3.20'

Update to upstream version '0.3.20'
with Debian dir 7fb92572900fe2cb77424212b77819cba4b157cd
- - - - -
8d5e96ce by Steffen Moeller at 2021-09-03T16:16:28+02:00
Initial series of updates.

- - - - -


16 changed files:

- + .github/workflows/python-package.yml
- − Pipfile
- − Pipfile.lock
- + condarecipe/epimodels/meta.yaml
- debian/changelog
- debian/control
- debian/patches/ignore_pyscaffold.patch
- debian/upstream/metadata
- debian/watch
- docs/Makefile
- docs/conf.py
- requirements.txt
- setup.cfg
- setup.py
- src/epimodels/__init__.py
- src/epimodels/tools/phase.py


Changes:

=====================================
.github/workflows/python-package.yml
=====================================
@@ -0,0 +1,39 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python package
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+
+    steps:
+    - uses: actions/checkout at v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python at v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest


=====================================
Pipfile deleted
=====================================
@@ -1,22 +0,0 @@
-[[source]]
-url = "https://pypi.org/simple"
-verify_ssl = true
-name = "pypi"
-
-[packages]
-cython = "*"
-numpy = "*"
-scipy = "*"
-sympy = "*"
-pytest = "*"
-pytest-cov = "*"
-matplotlib = "*"
-mypy = "*"
-sphinx = "*"
-pyitlib = "*"
-numba = "*"
-
-[dev-packages]
-
-[requires]
-python_version = "3.7"


=====================================
Pipfile.lock deleted
=====================================
@@ -1,593 +0,0 @@
-{
-    "_meta": {
-        "hash": {
-            "sha256": "f01b67c1332d4198903f615d8ae0bd93c3504172ad738a8481a3305c70f3a087"
-        },
-        "pipfile-spec": 6,
-        "requires": {
-            "python_version": "3.7"
-        },
-        "sources": [
-            {
-                "name": "pypi",
-                "url": "https://pypi.org/simple",
-                "verify_ssl": true
-            }
-        ]
-    },
-    "default": {
-        "alabaster": {
-            "hashes": [
-                "sha256:446438bdcca0e05bd45ea2de1668c1d9b032e1a9154c2c259092d77031ddd359",
-                "sha256:a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02"
-            ],
-            "version": "==0.7.12"
-        },
-        "atomicwrites": {
-            "hashes": [
-                "sha256:03472c30eb2c5d1ba9227e4c2ca66ab8287fbfbbda3888aa93dc2e28fc6811b4",
-                "sha256:75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6"
-            ],
-            "version": "==1.3.0"
-        },
-        "attrs": {
-            "hashes": [
-                "sha256:69c0dbf2ed392de1cb5ec704444b08a5ef81680a61cb899dc08127123af36a79",
-                "sha256:f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399"
-            ],
-            "version": "==19.1.0"
-        },
-        "babel": {
-            "hashes": [
-                "sha256:af92e6106cb7c55286b25b38ad7695f8b4efb36a90ba483d7f7a6628c46158ab",
-                "sha256:e86135ae101e31e2c8ec20a4e0c5220f4eed12487d5cf3f78be7e98d3a57fc28"
-            ],
-            "version": "==2.7.0"
-        },
-        "certifi": {
-            "hashes": [
-                "sha256:046832c04d4e752f37383b628bc601a7ea7211496b4638f6514d0e5b9acc4939",
-                "sha256:945e3ba63a0b9f577b1395204e13c3a231f9bc0223888be653286534e5873695"
-            ],
-            "version": "==2019.6.16"
-        },
-        "chardet": {
-            "hashes": [
-                "sha256:84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae",
-                "sha256:fc323ffcaeaed0e0a02bf4d117757b98aed530d9ed4531e3e15460124c106691"
-            ],
-            "version": "==3.0.4"
-        },
-        "coverage": {
-            "hashes": [
-                "sha256:08907593569fe59baca0bf152c43f3863201efb6113ecb38ce7e97ce339805a6",
-                "sha256:0be0f1ed45fc0c185cfd4ecc19a1d6532d72f86a2bac9de7e24541febad72650",
-                "sha256:141f08ed3c4b1847015e2cd62ec06d35e67a3ac185c26f7635f4406b90afa9c5",
-                "sha256:19e4df788a0581238e9390c85a7a09af39c7b539b29f25c89209e6c3e371270d",
-                "sha256:23cc09ed395b03424d1ae30dcc292615c1372bfba7141eb85e11e50efaa6b351",
-                "sha256:245388cda02af78276b479f299bbf3783ef0a6a6273037d7c60dc73b8d8d7755",
-                "sha256:331cb5115673a20fb131dadd22f5bcaf7677ef758741312bee4937d71a14b2ef",
-                "sha256:386e2e4090f0bc5df274e720105c342263423e77ee8826002dcffe0c9533dbca",
-                "sha256:3a794ce50daee01c74a494919d5ebdc23d58873747fa0e288318728533a3e1ca",
-                "sha256:60851187677b24c6085248f0a0b9b98d49cba7ecc7ec60ba6b9d2e5574ac1ee9",
-                "sha256:63a9a5fc43b58735f65ed63d2cf43508f462dc49857da70b8980ad78d41d52fc",
-                "sha256:6b62544bb68106e3f00b21c8930e83e584fdca005d4fffd29bb39fb3ffa03cb5",
-                "sha256:6ba744056423ef8d450cf627289166da65903885272055fb4b5e113137cfa14f",
-                "sha256:7494b0b0274c5072bddbfd5b4a6c6f18fbbe1ab1d22a41e99cd2d00c8f96ecfe",
-                "sha256:826f32b9547c8091679ff292a82aca9c7b9650f9fda3e2ca6bf2ac905b7ce888",
-                "sha256:93715dffbcd0678057f947f496484e906bf9509f5c1c38fc9ba3922893cda5f5",
-                "sha256:9a334d6c83dfeadae576b4d633a71620d40d1c379129d587faa42ee3e2a85cce",
-                "sha256:af7ed8a8aa6957aac47b4268631fa1df984643f07ef00acd374e456364b373f5",
-                "sha256:bf0a7aed7f5521c7ca67febd57db473af4762b9622254291fbcbb8cd0ba5e33e",
-                "sha256:bf1ef9eb901113a9805287e090452c05547578eaab1b62e4ad456fcc049a9b7e",
-                "sha256:c0afd27bc0e307a1ffc04ca5ec010a290e49e3afbe841c5cafc5c5a80ecd81c9",
-                "sha256:dd579709a87092c6dbee09d1b7cfa81831040705ffa12a1b248935274aee0437",
-                "sha256:df6712284b2e44a065097846488f66840445eb987eb81b3cc6e4149e7b6982e1",
-                "sha256:e07d9f1a23e9e93ab5c62902833bf3e4b1f65502927379148b6622686223125c",
-                "sha256:e2ede7c1d45e65e209d6093b762e98e8318ddeff95317d07a27a2140b80cfd24",
-                "sha256:e4ef9c164eb55123c62411f5936b5c2e521b12356037b6e1c2617cef45523d47",
-                "sha256:eca2b7343524e7ba246cab8ff00cab47a2d6d54ada3b02772e908a45675722e2",
-                "sha256:eee64c616adeff7db37cc37da4180a3a5b6177f5c46b187894e633f088fb5b28",
-                "sha256:ef824cad1f980d27f26166f86856efe11eff9912c4fed97d3804820d43fa550c",
-                "sha256:efc89291bd5a08855829a3c522df16d856455297cf35ae827a37edac45f466a7",
-                "sha256:fa964bae817babece5aa2e8c1af841bebb6d0b9add8e637548809d040443fee0",
-                "sha256:ff37757e068ae606659c28c3bd0d923f9d29a85de79bf25b2b34b148473b5025"
-            ],
-            "version": "==4.5.4"
-        },
-        "cycler": {
-            "hashes": [
-                "sha256:1d8a5ae1ff6c5cf9b93e8811e581232ad8920aeec647c37316ceac982b08cb2d",
-                "sha256:cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8"
-            ],
-            "version": "==0.10.0"
-        },
-        "cython": {
-            "hashes": [
-                "sha256:07efba7b32c082c519b75e3b03821c2f32848e2b3e9986c784bbd8ffaf0666d7",
-                "sha256:08db41daf18fabf7b7a85e39aa26954f6246994540043194af026c0df65a4942",
-                "sha256:19bbe3caf885a1d2e2c30eacc10d1e45dbbefb156493fe1d5d1adc1668cc1269",
-                "sha256:1c574f2f2ba760b82b2bcf6262e77e75589247dc5ef796a3ff1b2213e50ee452",
-                "sha256:1dfe672c686e34598bdbaa93c3b30acb3720ae9258232a4f68ba04ee9969063d",
-                "sha256:283faea84e6c4e54c3f5c8ff89aa2b6c1c3a813aad4f6d48ed3b9cc9043ef9f9",
-                "sha256:2a145888d0942e7c36e86a7b7c7e2923cb9f7055805a3b72dcb137e3efdb0979",
-                "sha256:3f75065936e16569d6e13dfd76de988f5eabeae460aa54770c9b961ab6f747fc",
-                "sha256:4d78124f5f281f1d5d5b7919cbbc65a7073ff93562def81ee78a8307e6e72494",
-                "sha256:5ba4d088b8e5d59b8a5911ca9c72952acf3c83296b57daf75af92fb2af1e8423",
-                "sha256:6b19daeda1d5d1dfc973b291246f6a63a663b20c33980724d6d073c562719536",
-                "sha256:790c7dc80fd1c3e38acefe06027e2f5a8466c128c7e47c6e140fd5316132574d",
-                "sha256:7f8c4e648881454ba3ba0bcf3b21a9e1878a67d20ea2b8d9ec1c4c628592ab6b",
-                "sha256:8bcd3f597290f9902548d6355898d7e376e7f3762f89db9cd50b2b58429df9e8",
-                "sha256:8ffb18f71972a5c718a8600d9f52e3507f0d6fb72a978e03270d34a7035c98fb",
-                "sha256:92f025df1cb391e09f65775598c7dfb7efad72d74713775db54e267f62ca94a1",
-                "sha256:93cf1c72472a2fd0ef4c52f6074dab08fc28d475b9c824ba73a52701f7a48ae1",
-                "sha256:9a7fa692cdc967fdbf6a053c1975137d01f6935dede2ef222c71840b290caf79",
-                "sha256:a68eb0c1375f2401de881692b30370a51e550052b8e346b2f71bbdbdc74a214f",
-                "sha256:ac3b7a12ddd52ea910ee3a041e6bc65df7a52f0ba7bd10fb7123502af482c152",
-                "sha256:b402b700edaf571a0bae18ec35d5b71c266873a6616412b672435c10b6d8f041",
-                "sha256:c29d069a4a30f472482343c866f7486731ad638ef9af92bfe5fca9c7323d638e",
-                "sha256:d822311498f185db449b687336b4e5db7638c8d8b03bdf10ae91d74e23c7cc0c",
-                "sha256:dccc8df9e1ac158b06777bbaaeb4516f245f9b147701ae25e6023960e4a0c2a3",
-                "sha256:e31f4b946c2765b2f35440fdb4b00c496dfc5babc53c7ae61966b41171d1d59f",
-                "sha256:eb43f9e582cc221ee2832e25ea6fe5c06f2acc9da6353c562e922f107db12af8",
-                "sha256:f07822248110fd6213db8bc2745fdbbccef6f2b3d18ac91a7fba29c6bc575da5",
-                "sha256:ff69854f123b959d4ae14bd5330714bb9ee4360052992dc0fbd0a3dee4261f95"
-            ],
-            "index": "pypi",
-            "version": "==0.29.13"
-        },
-        "docutils": {
-            "hashes": [
-                "sha256:6c4f696463b79f1fb8ba0c594b63840ebd41f059e92b31957c46b74a4599b6d0",
-                "sha256:9e4d7ecfc600058e07ba661411a2b7de2fd0fafa17d1a7f7361cd47b1175c827",
-                "sha256:a2aeea129088da402665e92e0b25b04b073c04b2dce4ab65caaa38b7ce2e1a99"
-            ],
-            "version": "==0.15.2"
-        },
-        "future": {
-            "hashes": [
-                "sha256:67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8"
-            ],
-            "version": "==0.17.1"
-        },
-        "idna": {
-            "hashes": [
-                "sha256:c357b3f628cf53ae2c4c05627ecc484553142ca23264e593d327bcde5e9c3407",
-                "sha256:ea8b7f6188e6fa117537c3df7da9fc686d485087abf6ac197f9c46432f7e4a3c"
-            ],
-            "version": "==2.8"
-        },
-        "imagesize": {
-            "hashes": [
-                "sha256:3f349de3eb99145973fefb7dbe38554414e5c30abd0c8e4b970a7c9d09f3a1d8",
-                "sha256:f3832918bc3c66617f92e35f5d70729187676313caa60c187eb0f28b8fe5e3b5"
-            ],
-            "version": "==1.1.0"
-        },
-        "importlib-metadata": {
-            "hashes": [
-                "sha256:0c505102757e7fa28b9f0958d8bc81301159dea16e2649858c92edc158b78a83",
-                "sha256:9a9f75ce32e78170905888acbf2376a81d3f21ecb3bb4867050413411d3ca7a9"
-            ],
-            "markers": "python_version < '3.8'",
-            "version": "==0.21"
-        },
-        "jinja2": {
-            "hashes": [
-                "sha256:065c4f02ebe7f7cf559e49ee5a95fb800a9e4528727aec6f24402a5374c65013",
-                "sha256:14dd6caf1527abb21f08f86c784eac40853ba93edb79552aa1e4b8aef1b61c7b"
-            ],
-            "version": "==2.10.1"
-        },
-        "joblib": {
-            "hashes": [
-                "sha256:21e0c34a69ad7fde4f2b1f3402290e9ec46f545f15f1541c582edfe05d87b63a",
-                "sha256:315d6b19643ec4afd4c41c671f9f2d65ea9d787da093487a81ead7b0bac94524"
-            ],
-            "version": "==0.13.2"
-        },
-        "kiwisolver": {
-            "hashes": [
-                "sha256:05b5b061e09f60f56244adc885c4a7867da25ca387376b02c1efc29cc16bcd0f",
-                "sha256:26f4fbd6f5e1dabff70a9ba0d2c4bd30761086454aa30dddc5b52764ee4852b7",
-                "sha256:3b2378ad387f49cbb328205bda569b9f87288d6bc1bf4cd683c34523a2341efe",
-                "sha256:400599c0fe58d21522cae0e8b22318e09d9729451b17ee61ba8e1e7c0346565c",
-                "sha256:47b8cb81a7d18dbaf4fed6a61c3cecdb5adec7b4ac292bddb0d016d57e8507d5",
-                "sha256:53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75",
-                "sha256:58e626e1f7dfbb620d08d457325a4cdac65d1809680009f46bf41eaf74ad0187",
-                "sha256:5a52e1b006bfa5be04fe4debbcdd2688432a9af4b207a3f429c74ad625022641",
-                "sha256:5c7ca4e449ac9f99b3b9d4693debb1d6d237d1542dd6a56b3305fe8a9620f883",
-                "sha256:682e54f0ce8f45981878756d7203fd01e188cc6c8b2c5e2cf03675390b4534d5",
-                "sha256:79bfb2f0bd7cbf9ea256612c9523367e5ec51d7cd616ae20ca2c90f575d839a2",
-                "sha256:7f4dd50874177d2bb060d74769210f3bce1af87a8c7cf5b37d032ebf94f0aca3",
-                "sha256:8944a16020c07b682df861207b7e0efcd2f46c7488619cb55f65882279119389",
-                "sha256:8aa7009437640beb2768bfd06da049bad0df85f47ff18426261acecd1cf00897",
-                "sha256:939f36f21a8c571686eb491acfffa9c7f1ac345087281b412d63ea39ca14ec4a",
-                "sha256:9733b7f64bd9f807832d673355f79703f81f0b3e52bfce420fc00d8cb28c6a6c",
-                "sha256:a02f6c3e229d0b7220bd74600e9351e18bc0c361b05f29adae0d10599ae0e326",
-                "sha256:a0c0a9f06872330d0dd31b45607197caab3c22777600e88031bfe66799e70bb0",
-                "sha256:acc4df99308111585121db217681f1ce0eecb48d3a828a2f9bbf9773f4937e9e",
-                "sha256:b64916959e4ae0ac78af7c3e8cef4becee0c0e9694ad477b4c6b3a536de6a544",
-                "sha256:d3fcf0819dc3fea58be1fd1ca390851bdb719a549850e708ed858503ff25d995",
-                "sha256:d52e3b1868a4e8fd18b5cb15055c76820df514e26aa84cc02f593d99fef6707f",
-                "sha256:db1a5d3cc4ae943d674718d6c47d2d82488ddd94b93b9e12d24aabdbfe48caee",
-                "sha256:e3a21a720791712ed721c7b95d433e036134de6f18c77dbe96119eaf7aa08004",
-                "sha256:e8bf074363ce2babeb4764d94f8e65efd22e6a7c74860a4f05a6947afc020ff2",
-                "sha256:f16814a4a96dc04bf1da7d53ee8d5b1d6decfc1a92a63349bb15d37b6a263dd9",
-                "sha256:f2b22153870ca5cf2ab9c940d7bc38e8e9089fa0f7e5856ea195e1cf4ff43d5a",
-                "sha256:f790f8b3dff3d53453de6a7b7ddd173d2e020fb160baff578d578065b108a05f"
-            ],
-            "version": "==1.1.0"
-        },
-        "markupsafe": {
-            "hashes": [
-                "sha256:00bc623926325b26bb9605ae9eae8a215691f33cae5df11ca5424f06f2d1f473",
-                "sha256:09027a7803a62ca78792ad89403b1b7a73a01c8cb65909cd876f7fcebd79b161",
-                "sha256:09c4b7f37d6c648cb13f9230d847adf22f8171b1ccc4d5682398e77f40309235",
-                "sha256:1027c282dad077d0bae18be6794e6b6b8c91d58ed8a8d89a89d59693b9131db5",
-                "sha256:24982cc2533820871eba85ba648cd53d8623687ff11cbb805be4ff7b4c971aff",
-                "sha256:29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b",
-                "sha256:43a55c2930bbc139570ac2452adf3d70cdbb3cfe5912c71cdce1c2c6bbd9c5d1",
-                "sha256:46c99d2de99945ec5cb54f23c8cd5689f6d7177305ebff350a58ce5f8de1669e",
-                "sha256:500d4957e52ddc3351cabf489e79c91c17f6e0899158447047588650b5e69183",
-                "sha256:535f6fc4d397c1563d08b88e485c3496cf5784e927af890fb3c3aac7f933ec66",
-                "sha256:62fe6c95e3ec8a7fad637b7f3d372c15ec1caa01ab47926cfdf7a75b40e0eac1",
-                "sha256:6dd73240d2af64df90aa7c4e7481e23825ea70af4b4922f8ede5b9e35f78a3b1",
-                "sha256:717ba8fe3ae9cc0006d7c451f0bb265ee07739daf76355d06366154ee68d221e",
-                "sha256:79855e1c5b8da654cf486b830bd42c06e8780cea587384cf6545b7d9ac013a0b",
-                "sha256:7c1699dfe0cf8ff607dbdcc1e9b9af1755371f92a68f706051cc8c37d447c905",
-                "sha256:88e5fcfb52ee7b911e8bb6d6aa2fd21fbecc674eadd44118a9cc3863f938e735",
-                "sha256:8defac2f2ccd6805ebf65f5eeb132adcf2ab57aa11fdf4c0dd5169a004710e7d",
-                "sha256:98c7086708b163d425c67c7a91bad6e466bb99d797aa64f965e9d25c12111a5e",
-                "sha256:9add70b36c5666a2ed02b43b335fe19002ee5235efd4b8a89bfcf9005bebac0d",
-                "sha256:9bf40443012702a1d2070043cb6291650a0841ece432556f784f004937f0f32c",
-                "sha256:ade5e387d2ad0d7ebf59146cc00c8044acbd863725f887353a10df825fc8ae21",
-                "sha256:b00c1de48212e4cc9603895652c5c410df699856a2853135b3967591e4beebc2",
-                "sha256:b1282f8c00509d99fef04d8ba936b156d419be841854fe901d8ae224c59f0be5",
-                "sha256:b2051432115498d3562c084a49bba65d97cf251f5a331c64a12ee7e04dacc51b",
-                "sha256:ba59edeaa2fc6114428f1637ffff42da1e311e29382d81b339c1817d37ec93c6",
-                "sha256:c8716a48d94b06bb3b2524c2b77e055fb313aeb4ea620c8dd03a105574ba704f",
-                "sha256:cd5df75523866410809ca100dc9681e301e3c27567cf498077e8551b6d20e42f",
-                "sha256:e249096428b3ae81b08327a63a485ad0878de3fb939049038579ac0ef61e17e7"
-            ],
-            "version": "==1.1.1"
-        },
-        "matplotlib": {
-            "hashes": [
-                "sha256:1febd22afe1489b13c6749ea059d392c03261b2950d1d45c17e3aed812080c93",
-                "sha256:31a30d03f39528c79f3a592857be62a08595dec4ac034978ecd0f814fa0eec2d",
-                "sha256:4442ce720907f67a79d45de9ada47be81ce17e6c2f448b3c64765af93f6829c9",
-                "sha256:796edbd1182cbffa7e1e7a97f1e141f875a8501ba8dd834269ae3cd45a8c976f",
-                "sha256:934e6243df7165aad097572abf5b6003c77c9b6c480c3c4de6f2ef1b5fdd4ec0",
-                "sha256:bab9d848dbf1517bc58d1f486772e99919b19efef5dd8596d4b26f9f5ee08b6b",
-                "sha256:c1fe1e6cdaa53f11f088b7470c2056c0df7d80ee4858dadf6cbe433fcba4323b",
-                "sha256:e5b8aeca9276a3a988caebe9f08366ed519fff98f77c6df5b64d7603d0e42e36",
-                "sha256:ec6bd0a6a58df3628ff269978f4a4b924a0d371ad8ce1f8e2b635b99e482877a"
-            ],
-            "index": "pypi",
-            "version": "==3.1.1"
-        },
-        "more-itertools": {
-            "hashes": [
-                "sha256:409cd48d4db7052af495b09dec721011634af3753ae1ef92d2b32f73a745f832",
-                "sha256:92b8c4b06dac4f0611c0729b2f2ede52b2e1bac1ab48f089c7ddc12e26bb60c4"
-            ],
-            "version": "==7.2.0"
-        },
-        "mpmath": {
-            "hashes": [
-                "sha256:fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6"
-            ],
-            "version": "==1.1.0"
-        },
-        "mypy": {
-            "hashes": [
-                "sha256:0107bff4f46a289f0e4081d59b77cef1c48ea43da5a0dbf0005d54748b26df2a",
-                "sha256:07957f5471b3bb768c61f08690c96d8a09be0912185a27a68700f3ede99184e4",
-                "sha256:10af62f87b6921eac50271e667cc234162a194e742d8e02fc4ddc121e129a5b0",
-                "sha256:11fd60d2f69f0cefbe53ce551acf5b1cec1a89e7ce2d47b4e95a84eefb2899ae",
-                "sha256:15e43d3b1546813669bd1a6ec7e6a11d2888db938e0607f7b5eef6b976671339",
-                "sha256:352c24ba054a89bb9a35dd064ee95ab9b12903b56c72a8d3863d882e2632dc76",
-                "sha256:437020a39417e85e22ea8edcb709612903a9924209e10b3ec6d8c9f05b79f498",
-                "sha256:49925f9da7cee47eebf3420d7c0e00ec662ec6abb2780eb0a16260a7ba25f9c4",
-                "sha256:6724fcd5777aa6cebfa7e644c526888c9d639bd22edd26b2a8038c674a7c34bd",
-                "sha256:7a17613f7ea374ab64f39f03257f22b5755335b73251d0d253687a69029701ba",
-                "sha256:cdc1151ced496ca1496272da7fc356580e95f2682be1d32377c22ddebdf73c91"
-            ],
-            "index": "pypi",
-            "version": "==0.720"
-        },
-        "mypy-extensions": {
-            "hashes": [
-                "sha256:37e0e956f41369209a3d5f34580150bcacfabaa57b33a15c0b25f4b5725e0812",
-                "sha256:b16cabe759f55e3409a7d231ebd2841378fb0c27a5d1994719e340e4f429ac3e"
-            ],
-            "version": "==0.4.1"
-        },
-        "numpy": {
-            "hashes": [
-                "sha256:05dbfe72684cc14b92568de1bc1f41e5f62b00f714afc9adee42f6311738091f",
-                "sha256:0d82cb7271a577529d07bbb05cb58675f2deb09772175fab96dc8de025d8ac05",
-                "sha256:10132aa1fef99adc85a905d82e8497a580f83739837d7cbd234649f2e9b9dc58",
-                "sha256:12322df2e21f033a60c80319c25011194cd2a21294cc66fee0908aeae2c27832",
-                "sha256:16f19b3aa775dddc9814e02a46b8e6ae6a54ed8cf143962b4e53f0471dbd7b16",
-                "sha256:3d0b0989dd2d066db006158de7220802899a1e5c8cf622abe2d0bd158fd01c2c",
-                "sha256:438a3f0e7b681642898fd7993d38e2bf140a2d1eafaf3e89bb626db7f50db355",
-                "sha256:5fd214f482ab53f2cea57414c5fb3e58895b17df6e6f5bca5be6a0bb6aea23bb",
-                "sha256:73615d3edc84dd7c4aeb212fa3748fb83217e00d201875a47327f55363cef2df",
-                "sha256:7bd355ad7496f4ce1d235e9814ec81ee3d28308d591c067ce92e49f745ba2c2f",
-                "sha256:7d077f2976b8f3de08a0dcf5d72083f4af5411e8fddacd662aae27baa2601196",
-                "sha256:a4092682778dc48093e8bda8d26ee8360153e2047826f95a3f5eae09f0ae3abf",
-                "sha256:b458de8624c9f6034af492372eb2fee41a8e605f03f4732f43fc099e227858b2",
-                "sha256:e70fc8ff03a961f13363c2c95ef8285e0cf6a720f8271836f852cc0fa64e97c8",
-                "sha256:ee8e9d7cad5fe6dde50ede0d2e978d81eafeaa6233fb0b8719f60214cf226578",
-                "sha256:f4a4f6aba148858a5a5d546a99280f71f5ee6ec8182a7d195af1a914195b21a2"
-            ],
-            "index": "pypi",
-            "version": "==1.17.2"
-        },
-        "packaging": {
-            "hashes": [
-                "sha256:a7ac867b97fdc07ee80a8058fe4435ccd274ecc3b0ed61d852d7d53055528cf9",
-                "sha256:c491ca87294da7cc01902edbe30a5bc6c4c28172b5138ab4e4aa1b9d7bfaeafe"
-            ],
-            "version": "==19.1"
-        },
-        "pandas": {
-            "hashes": [
-                "sha256:18d91a9199d1dfaa01ad645f7540370ba630bdcef09daaf9edf45b4b1bca0232",
-                "sha256:3f26e5da310a0c0b83ea50da1fd397de2640b02b424aa69be7e0784228f656c9",
-                "sha256:4182e32f4456d2c64619e97c58571fa5ca0993d1e8c2d9ca44916185e1726e15",
-                "sha256:426e590e2eb0e60f765271d668a30cf38b582eaae5ec9b31229c8c3c10c5bc21",
-                "sha256:5eb934a8f0dc358f0e0cdf314072286bbac74e4c124b64371395e94644d5d919",
-                "sha256:717928808043d3ea55b9bcde636d4a52d2236c246f6df464163a66ff59980ad8",
-                "sha256:8145f97c5ed71827a6ec98ceaef35afed1377e2d19c4078f324d209ff253ecb5",
-                "sha256:8744c84c914dcc59cbbb2943b32b7664df1039d99e834e1034a3372acb89ea4d",
-                "sha256:c1ac1d9590d0c9314ebf01591bd40d4c03d710bfc84a3889e5263c97d7891dee",
-                "sha256:cb2e197b7b0687becb026b84d3c242482f20cbb29a9981e43604eb67576da9f6",
-                "sha256:d4001b71ad2c9b84ff18b182cea22b7b6cbf624216da3ea06fb7af28d1f93165",
-                "sha256:d8930772adccb2882989ab1493fa74bd87d47c8ac7417f5dd3dd834ba8c24dc9",
-                "sha256:dfbb0173ee2399bc4ed3caf2d236e5c0092f948aafd0a15fbe4a0e77ee61a958",
-                "sha256:eebfbba048f4fa8ac711b22c78516e16ff8117d05a580e7eeef6b0c2be554c18",
-                "sha256:f1b21bc5cf3dbea53d33615d1ead892dfdae9d7052fa8898083bec88be20dcd2"
-            ],
-            "version": "==0.25.1"
-        },
-        "pluggy": {
-            "hashes": [
-                "sha256:0825a152ac059776623854c1543d65a4ad408eb3d33ee114dff91e57ec6ae6fc",
-                "sha256:b9817417e95936bf75d85d3f8767f7df6cdde751fc40aed3bb3074cbcb77757c"
-            ],
-            "version": "==0.12.0"
-        },
-        "py": {
-            "hashes": [
-                "sha256:64f65755aee5b381cea27766a3a147c3f15b9b6b9ac88676de66ba2ae36793fa",
-                "sha256:dc639b046a6e2cff5bbe40194ad65936d6ba360b52b3c3fe1d08a82dd50b5e53"
-            ],
-            "version": "==1.8.0"
-        },
-        "pygments": {
-            "hashes": [
-                "sha256:71e430bc85c88a430f000ac1d9b331d2407f681d6f6aec95e8bcfbc3df5b0127",
-                "sha256:881c4c157e45f30af185c1ffe8d549d48ac9127433f2c380c24b84572ad66297"
-            ],
-            "version": "==2.4.2"
-        },
-        "pyitlib": {
-            "hashes": [
-                "sha256:746ee65704da29eb27623755bd330e796164509462e5357b4241f5c6965ea6eb"
-            ],
-            "index": "pypi",
-            "version": "==0.2.2"
-        },
-        "pyparsing": {
-            "hashes": [
-                "sha256:6f98a7b9397e206d78cc01df10131398f1c8b8510a2f4d97d9abd82e1aacdd80",
-                "sha256:d9338df12903bbf5d65a0e4e87c2161968b10d2e489652bb47001d82a9b028b4"
-            ],
-            "version": "==2.4.2"
-        },
-        "pytest": {
-            "hashes": [
-                "sha256:95d13143cc14174ca1a01ec68e84d76ba5d9d493ac02716fd9706c949a505210",
-                "sha256:b78fe2881323bd44fd9bd76e5317173d4316577e7b1cddebae9136a4495ec865"
-            ],
-            "index": "pypi",
-            "version": "==5.1.2"
-        },
-        "pytest-cov": {
-            "hashes": [
-                "sha256:2b097cde81a302e1047331b48cadacf23577e431b61e9c6f49a1170bbe3d3da6",
-                "sha256:e00ea4fdde970725482f1f35630d12f074e121a23801aabf2ae154ec6bdd343a"
-            ],
-            "index": "pypi",
-            "version": "==2.7.1"
-        },
-        "python-dateutil": {
-            "hashes": [
-                "sha256:7e6584c74aeed623791615e26efd690f29817a27c73085b78e4bad02493df2fb",
-                "sha256:c89805f6f4d64db21ed966fda138f8a5ed7a4fdbc1a8ee329ce1b74e3c74da9e"
-            ],
-            "version": "==2.8.0"
-        },
-        "pytz": {
-            "hashes": [
-                "sha256:26c0b32e437e54a18161324a2fca3c4b9846b74a8dccddd843113109e1116b32",
-                "sha256:c894d57500a4cd2d5c71114aaab77dbab5eabd9022308ce5ac9bb93a60a6f0c7"
-            ],
-            "version": "==2019.2"
-        },
-        "requests": {
-            "hashes": [
-                "sha256:11e007a8a2aa0323f5a921e9e6a2d7e4e67d9877e85773fba9ba6419025cbeb4",
-                "sha256:9cf5292fcd0f598c671cfc1e0d7d1a7f13bb8085e9a590f48c010551dc6c4b31"
-            ],
-            "version": "==2.22.0"
-        },
-        "scikit-learn": {
-            "hashes": [
-                "sha256:1ac81293d261747c25ea5a0ee8cd2bb1f3b5ba9ec05421a7f9f0feb4eb7c4116",
-                "sha256:289361cf003d90b007f5066b27fcddc2d71324c82f1c88e316fedacb0dfdd516",
-                "sha256:3a14d0abd4281fc3fd2149c486c3ec7cedad848b8d5f7b6f61522029d65a29f8",
-                "sha256:5083a5e50d9d54548e4ada829598ae63a05651dd2bb319f821ffd9e8388384a6",
-                "sha256:777cdd5c077b7ca9cb381396c81990cf41d2fa8350760d3cad3b4c460a7db644",
-                "sha256:8bf2ff63da820d09b96b18e88f9625228457bff8df4618f6b087e12442ef9e15",
-                "sha256:8d319b71c449627d178f21c57614e21747e54bb3fc9602b6f42906c3931aa320",
-                "sha256:928050b65781fea9542dfe9bfe02d8c4f5530baa8472ec60782ea77347d2c836",
-                "sha256:92c903613ff50e22aa95d589f9fff5deb6f34e79f7f21f609680087f137bb524",
-                "sha256:ae322235def5ce8fae645b439e332e6f25d34bb90d6a6c8e261f17eb476457b7",
-                "sha256:c1cd6b29eb1fd1cc672ac5e4a8be5f6ea936d094a3dc659ada0746d6fac750b1",
-                "sha256:c41a6e2685d06bcdb0d26533af2540f54884d40db7e48baed6a5bcbf1a7cc642",
-                "sha256:d07fcb0c0acbc043faa0e7cf4d2037f71193de3fb04fb8ed5c259b089af1cf5c",
-                "sha256:d146d5443cda0a41f74276e42faf8c7f283fef49e8a853b832885239ef544e05",
-                "sha256:eb2b7bed0a26ba5ce3700e15938b28a4f4513578d3e54a2156c29df19ac5fd01",
-                "sha256:eb9b8ebf59eddd8b96366428238ab27d05a19e89c5516ce294abc35cea75d003"
-            ],
-            "version": "==0.21.3"
-        },
-        "scipy": {
-            "hashes": [
-                "sha256:0baa64bf42592032f6f6445a07144e355ca876b177f47ad8d0612901c9375bef",
-                "sha256:243b04730d7223d2b844bda9500310eecc9eda0cba9ceaf0cde1839f8287dfa8",
-                "sha256:2643cfb46d97b7797d1dbdb6f3c23fe3402904e3c90e6facfe6a9b98d808c1b5",
-                "sha256:396eb4cdad421f846a1498299474f0a3752921229388f91f60dc3eda55a00488",
-                "sha256:3ae3692616975d3c10aca6d574d6b4ff95568768d4525f76222fb60f142075b9",
-                "sha256:435d19f80b4dcf67dc090cc04fde2c5c8a70b3372e64f6a9c58c5b806abfa5a8",
-                "sha256:46a5e55850cfe02332998b3aef481d33f1efee1960fe6cfee0202c7dd6fc21ab",
-                "sha256:75b513c462e58eeca82b22fc00f0d1875a37b12913eee9d979233349fce5c8b2",
-                "sha256:7ccfa44a08226825126c4ef0027aa46a38c928a10f0a8a8483c80dd9f9a0ad44",
-                "sha256:89dd6a6d329e3f693d1204d5562dd63af0fd7a17854ced17f9cbc37d5b853c8d",
-                "sha256:a81da2fe32f4eab8b60d56ad43e44d93d392da228a77e229e59b51508a00299c",
-                "sha256:a9d606d11eb2eec7ef893eb825017fbb6eef1e1d0b98a5b7fc11446ebeb2b9b1",
-                "sha256:ac37eb652248e2d7cbbfd89619dce5ecfd27d657e714ed049d82f19b162e8d45",
-                "sha256:cbc0611699e420774e945f6a4e2830f7ca2b3ee3483fca1aa659100049487dd5",
-                "sha256:d02d813ec9958ed63b390ded463163685af6025cb2e9a226ec2c477df90c6957",
-                "sha256:dd3b52e00f93fd1c86f2d78243dfb0d02743c94dd1d34ffea10055438e63b99d"
-            ],
-            "index": "pypi",
-            "version": "==1.3.1"
-        },
-        "six": {
-            "hashes": [
-                "sha256:3350809f0555b11f552448330d0b52d5f24c91a322ea4a15ef22629740f3761c",
-                "sha256:d16a0141ec1a18405cd4ce8b4613101da75da0e9a7aec5bdd4fa804d0e0eba73"
-            ],
-            "version": "==1.12.0"
-        },
-        "snowballstemmer": {
-            "hashes": [
-                "sha256:713e53b79cbcf97bc5245a06080a33d54a77e7cce2f789c835a143bcdb5c033e"
-            ],
-            "version": "==1.9.1"
-        },
-        "sphinx": {
-            "hashes": [
-                "sha256:0d586b0f8c2fc3cc6559c5e8fd6124628110514fda0e5d7c82e682d749d2e845",
-                "sha256:839a3ed6f6b092bb60f492024489cc9e6991360fb9f52ed6361acd510d261069"
-            ],
-            "index": "pypi",
-            "version": "==2.2.0"
-        },
-        "sphinxcontrib-applehelp": {
-            "hashes": [
-                "sha256:edaa0ab2b2bc74403149cb0209d6775c96de797dfd5b5e2a71981309efab3897",
-                "sha256:fb8dee85af95e5c30c91f10e7eb3c8967308518e0f7488a2828ef7bc191d0d5d"
-            ],
-            "version": "==1.0.1"
-        },
-        "sphinxcontrib-devhelp": {
-            "hashes": [
-                "sha256:6c64b077937330a9128a4da74586e8c2130262f014689b4b89e2d08ee7294a34",
-                "sha256:9512ecb00a2b0821a146736b39f7aeb90759834b07e81e8cc23a9c70bacb9981"
-            ],
-            "version": "==1.0.1"
-        },
-        "sphinxcontrib-htmlhelp": {
-            "hashes": [
-                "sha256:4670f99f8951bd78cd4ad2ab962f798f5618b17675c35c5ac3b2132a14ea8422",
-                "sha256:d4fd39a65a625c9df86d7fa8a2d9f3cd8299a3a4b15db63b50aac9e161d8eff7"
-            ],
-            "version": "==1.0.2"
-        },
-        "sphinxcontrib-jsmath": {
-            "hashes": [
-                "sha256:2ec2eaebfb78f3f2078e73666b1415417a116cc848b72e5172e596c871103178",
-                "sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8"
-            ],
-            "version": "==1.0.1"
-        },
-        "sphinxcontrib-qthelp": {
-            "hashes": [
-                "sha256:513049b93031beb1f57d4daea74068a4feb77aa5630f856fcff2e50de14e9a20",
-                "sha256:79465ce11ae5694ff165becda529a600c754f4bc459778778c7017374d4d406f"
-            ],
-            "version": "==1.0.2"
-        },
-        "sphinxcontrib-serializinghtml": {
-            "hashes": [
-                "sha256:c0efb33f8052c04fd7a26c0a07f1678e8512e0faec19f4aa8f2473a8b81d5227",
-                "sha256:db6615af393650bf1151a6cd39120c29abaf93cc60db8c48eb2dddbfdc3a9768"
-            ],
-            "version": "==1.1.3"
-        },
-        "sympy": {
-            "hashes": [
-                "sha256:71a11e5686ae7ab6cb8feb5bd2651ef4482f8fd43a7c27e645a165e4353b23e1",
-                "sha256:f9b00ec76151c98470e84f1da2d7d03633180b71fb318428ddccce1c867d3eaa"
-            ],
-            "index": "pypi",
-            "version": "==1.4"
-        },
-        "typed-ast": {
-            "hashes": [
-                "sha256:18511a0b3e7922276346bcb47e2ef9f38fb90fd31cb9223eed42c85d1312344e",
-                "sha256:262c247a82d005e43b5b7f69aff746370538e176131c32dda9cb0f324d27141e",
-                "sha256:2b907eb046d049bcd9892e3076c7a6456c93a25bebfe554e931620c90e6a25b0",
-                "sha256:354c16e5babd09f5cb0ee000d54cfa38401d8b8891eefa878ac772f827181a3c",
-                "sha256:4e0b70c6fc4d010f8107726af5fd37921b666f5b31d9331f0bd24ad9a088e631",
-                "sha256:630968c5cdee51a11c05a30453f8cd65e0cc1d2ad0d9192819df9978984529f4",
-                "sha256:66480f95b8167c9c5c5c87f32cf437d585937970f3fc24386f313a4c97b44e34",
-                "sha256:71211d26ffd12d63a83e079ff258ac9d56a1376a25bc80b1cdcdf601b855b90b",
-                "sha256:95bd11af7eafc16e829af2d3df510cecfd4387f6453355188342c3e79a2ec87a",
-                "sha256:bc6c7d3fa1325a0c6613512a093bc2a2a15aeec350451cbdf9e1d4bffe3e3233",
-                "sha256:cc34a6f5b426748a507dd5d1de4c1978f2eb5626d51326e43280941206c209e1",
-                "sha256:d755f03c1e4a51e9b24d899561fec4ccaf51f210d52abdf8c07ee2849b212a36",
-                "sha256:d7c45933b1bdfaf9f36c579671fec15d25b06c8398f113dab64c18ed1adda01d",
-                "sha256:d896919306dd0aa22d0132f62a1b78d11aaf4c9fc5b3410d3c666b818191630a",
-                "sha256:ffde2fbfad571af120fcbfbbc61c72469e72f550d676c3342492a9dfdefb8f12"
-            ],
-            "version": "==1.4.0"
-        },
-        "typing-extensions": {
-            "hashes": [
-                "sha256:2ed632b30bb54fc3941c382decfd0ee4148f5c591651c9272473fea2c6397d95",
-                "sha256:b1edbbf0652660e32ae780ac9433f4231e7339c7f9a8057d0f042fcbcea49b87",
-                "sha256:d8179012ec2c620d3791ca6fe2bf7979d979acdbef1fca0bc56b37411db682ed"
-            ],
-            "version": "==3.7.4"
-        },
-        "urllib3": {
-            "hashes": [
-                "sha256:b246607a25ac80bedac05c6f282e3cdaf3afb65420fd024ac94435cabe6e18d1",
-                "sha256:dbe59173209418ae49d485b87d1681aefa36252ee85884c31346debd19463232"
-            ],
-            "version": "==1.25.3"
-        },
-        "wcwidth": {
-            "hashes": [
-                "sha256:3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e",
-                "sha256:f4ebe71925af7b40a864553f761ed559b43544f8f71746c2d756c7fe788ade7c"
-            ],
-            "version": "==0.1.7"
-        },
-        "zipp": {
-            "hashes": [
-                "sha256:3718b1cbcd963c7d4c5511a8240812904164b7f381b647143a89d3b98f9bcd8e",
-                "sha256:f06903e9f1f43b12d371004b4ac7b06ab39a44adc747266928ae6debfa7b3335"
-            ],
-            "version": "==0.6.0"
-        }
-    },
-    "develop": {}
-}


=====================================
condarecipe/epimodels/meta.yaml
=====================================
@@ -0,0 +1,34 @@
+{% set name = "epimodels" %}
+{% set version = "0.3.19" %}
+
+package:
+  name: "{{ name|lower }}"
+  version: "{{ version }}"
+
+source:
+  url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
+  sha256: 8dec0de96e6ec506e3c61b7af6d687791c6db0eb5f74a90538f2844505db60e8
+
+build:
+  number: 0
+  script: "{{ PYTHON }} -m pip install . -vv"
+
+requirements:
+  host:
+    - pip
+    - python
+  run:
+    - python
+
+about:
+  home: The package home page
+  license: mit
+  license_family: MIT
+  license_file: 
+  summary: "Library of mathematical epidemic models for use in simulation studies and inference"
+  doc_url: 
+  dev_url: 
+
+extra:
+  recipe-maintainers:
+    - your-github-id-here


=====================================
debian/changelog
=====================================
@@ -1,3 +1,21 @@
+python-epimodels (0.3.20-1) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * d/u/metadata: Added ref to conda
+  * Standards-Version: 4.6.0 (routine-update)
+  
+  TODO: Tests fail because of failing X connection?!?
+
+ -- Steffen Moeller <moeller at debian.org>  Fri, 03 Sep 2021 16:06:49 +0200
+
+python-epimodels (0.3.18-3.1) UNRELEASED; urgency=medium
+
+  * Non-maintainer upload.
+  * Fix watchfile to detect new versions on github (routine-update)
+
+ -- Steffen Moeller <moeller at debian.org>  Fri, 03 Sep 2021 16:06:46 +0200
+
 python-epimodels (0.3.18-3) unstable; urgency=medium
 
   * Team Upload.


=====================================
debian/control
=====================================
@@ -12,7 +12,7 @@ Build-Depends: debhelper-compat (= 13),
                python3-scipy <!nocheck>,
                python3-pytest <!nocheck>,
                python3-pytest-cov <!nocheck>
-Standards-Version: 4.5.1
+Standards-Version: 4.6.0
 Vcs-Browser: https://salsa.debian.org/med-team/python-epimodels
 Vcs-Git: https://salsa.debian.org/med-team/python-epimodels.git
 Homepage: https://github.com/fccoelho/epimodels


=====================================
debian/patches/ignore_pyscaffold.patch
=====================================
@@ -2,32 +2,16 @@ Author: Andreas Tille <tille at debian.org>
 Last-Update: Sun, 21 Feb 2021 18:38:03 +0100
 Description: Avoid usage of pyscaffold
 
---- a/setup.py
-+++ b/setup.py
-@@ -20,4 +20,4 @@ except VersionConflict:
- 
- 
- if __name__ == "__main__":
--    setup(use_pyscaffold=True)
-+    setup(use_pyscaffold=False)
---- a/setup.cfg
-+++ b/setup.cfg
-@@ -25,7 +25,7 @@ include_package_data = True
- package_dir =
-     =src
- # DON'T CHANGE THE FOLLOWING LINE! IT WILL BE UPDATED BY PYSCAFFOLD!
--setup_requires = pyscaffold>=3.2a0,<3.3a0
-+# setup_requires = pyscaffold>=3.2a0,<3.3a0
- # Add here dependencies of your project (semicolon/line-separated), e.g..
- install_requires = numpy; scipy; cython
- # The usage of test_requires is discouraged, see `Dependency Management` docs
-@@ -77,24 +77,10 @@ norecursedirs =
+Index: python-epimodels/setup.cfg
+===================================================================
+--- python-epimodels.orig/setup.cfg
++++ python-epimodels/setup.cfg
+@@ -80,25 +80,10 @@ norecursedirs =
      .tox
  testpaths = tests
  
 -[aliases]
--build = bdist_wheel
--release = build upload
+-release = sdist bdist_wheel upload
 -
 -[bdist_wheel]
 -# Use this option if your package is pure-python
@@ -41,17 +25,20 @@ Description: Avoid usage of pyscaffold
 -# Options for the devpi: PyPI server and packaging tool
 -# VCS export must be deactivated since we are using setuptools-scm
 -no-vcs = 1
--formats = bdist_wheel
+-formats =
+-    sdist
+-    bdist_wheel
 -
  [flake8]
  # Some sane defaults for the code style checker flake8
  exclude =
-@@ -104,8 +90,3 @@ exclude =
+@@ -107,9 +92,3 @@ exclude =
+     dist
      .eggs
      docs/conf.py
- 
+-
 -[pyscaffold]
 -# PyScaffold's parameters when the project was created.
 -# This will be used when updating. Do not change!
--version = 3.2.3
+-version = 4.0
 -package = epimodels


=====================================
debian/upstream/metadata
=====================================
@@ -3,3 +3,9 @@ Bug-Database: https://github.com/fccoelho/epimodels/issues
 Bug-Submit: https://github.com/fccoelho/epimodels/issues/new
 Repository: https://github.com/fccoelho/epimodels.git
 Repository-Browse: https://github.com/fccoelho/epimodels
+Registry:
+ - Name: conda:fccoelho
+   Entry: epimodels
+ - Name: bio.tools
+   Entry: NA
+   Checked: 2021-09-03


=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
 version=4
 
 opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
-  https://github.com/fccoelho/epimodels/releases .*/archive/v?@ANY_VERSION@\.tar\.gz
+  https://github.com/fccoelho/epimodels/releases .*/v?@ANY_VERSION@\.tar\.gz


=====================================
docs/Makefile
=====================================
@@ -1,193 +1,29 @@
 # Makefile for Sphinx documentation
 #
 
-# You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = sphinx-build
-PAPER         =
-BUILDDIR      = ../build/sphinx/
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
 AUTODOCDIR    = api
-AUTODOCBUILD  = sphinx-apidoc
-PROJECT       = epimodels
-MODULEDIR     = ../src/epimodels
 
 # User-friendly check for sphinx-build
 ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $?), 1)
-$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+$(error "The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/")
 endif
 
-# Internal variables.
-PAPEROPT_a4     = -D latex_paper_size=a4
-PAPEROPT_letter = -D latex_paper_size=letter
-ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
-# the i18n builder cannot share the environment and doctrees with the others
-I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
-
-.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext doc-requirements
+.PHONY: help clean Makefile
 
+# Put it first so that "make" without argument is like "make help".
 help:
-	@echo "Please use \`make <target>' where <target> is one of"
-	@echo "  html       to make standalone HTML files"
-	@echo "  dirhtml    to make HTML files named index.html in directories"
-	@echo "  singlehtml to make a single large HTML file"
-	@echo "  pickle     to make pickle files"
-	@echo "  json       to make JSON files"
-	@echo "  htmlhelp   to make HTML files and a HTML help project"
-	@echo "  qthelp     to make HTML files and a qthelp project"
-	@echo "  devhelp    to make HTML files and a Devhelp project"
-	@echo "  epub       to make an epub"
-	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
-	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
-	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
-	@echo "  text       to make text files"
-	@echo "  man        to make manual pages"
-	@echo "  texinfo    to make Texinfo files"
-	@echo "  info       to make Texinfo files and run them through makeinfo"
-	@echo "  gettext    to make PO message catalogs"
-	@echo "  changes    to make an overview of all changed/added/deprecated items"
-	@echo "  xml        to make Docutils-native XML files"
-	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
-	@echo "  linkcheck  to check all external links for integrity"
-	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
 clean:
 	rm -rf $(BUILDDIR)/* $(AUTODOCDIR)
 
-$(AUTODOCDIR): $(MODULEDIR)
-	mkdir -p $@
-	$(AUTODOCBUILD) -f -o $@ $^
-
-doc-requirements: $(AUTODOCDIR)
-
-html: doc-requirements
-	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
-	@echo
-	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
-
-dirhtml: doc-requirements
-	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
-	@echo
-	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
-
-singlehtml: doc-requirements
-	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
-	@echo
-	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
-
-pickle: doc-requirements
-	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
-	@echo
-	@echo "Build finished; now you can process the pickle files."
-
-json: doc-requirements
-	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
-	@echo
-	@echo "Build finished; now you can process the JSON files."
-
-htmlhelp: doc-requirements
-	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
-	@echo
-	@echo "Build finished; now you can run HTML Help Workshop with the" \
-	      ".hhp project file in $(BUILDDIR)/htmlhelp."
-
-qthelp: doc-requirements
-	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
-	@echo
-	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
-	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
-	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/$(PROJECT).qhcp"
-	@echo "To view the help file:"
-	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/$(PROJECT).qhc"
-
-devhelp: doc-requirements
-	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
-	@echo
-	@echo "Build finished."
-	@echo "To view the help file:"
-	@echo "# mkdir -p $HOME/.local/share/devhelp/$(PROJECT)"
-	@echo "# ln -s $(BUILDDIR)/devhelp $HOME/.local/share/devhelp/$(PROJEC)"
-	@echo "# devhelp"
-
-epub: doc-requirements
-	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
-	@echo
-	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
-
-patch-latex:
-	find _build/latex -iname "*.tex" | xargs -- \
-		sed -i'' 's~includegraphics{~includegraphics\[keepaspectratio,max size={\\textwidth}{\\textheight}\]{~g'
-
-latex: doc-requirements
-	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
-	$(MAKE) patch-latex
-	@echo
-	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
-	@echo "Run \`make' in that directory to run these through (pdf)latex" \
-	      "(use \`make latexpdf' here to do that automatically)."
-
-latexpdf: doc-requirements
-	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
-	$(MAKE) patch-latex
-	@echo "Running LaTeX files through pdflatex..."
-	$(MAKE) -C $(BUILDDIR)/latex all-pdf
-	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
-
-latexpdfja: doc-requirements
-	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
-	@echo "Running LaTeX files through platex and dvipdfmx..."
-	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
-	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
-
-text: doc-requirements
-	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
-	@echo
-	@echo "Build finished. The text files are in $(BUILDDIR)/text."
-
-man: doc-requirements
-	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
-	@echo
-	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
-
-texinfo: doc-requirements
-	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
-	@echo
-	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
-	@echo "Run \`make' in that directory to run these through makeinfo" \
-	      "(use \`make info' here to do that automatically)."
-
-info: doc-requirements
-	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
-	@echo "Running Texinfo files through makeinfo..."
-	make -C $(BUILDDIR)/texinfo info
-	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
-
-gettext: doc-requirements
-	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
-	@echo
-	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
-
-changes: doc-requirements
-	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
-	@echo
-	@echo "The overview file is in $(BUILDDIR)/changes."
-
-linkcheck: doc-requirements
-	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
-	@echo
-	@echo "Link check complete; look for any errors in the above output " \
-	      "or in $(BUILDDIR)/linkcheck/output.txt."
-
-doctest: doc-requirements
-	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
-	@echo "Testing of doctests in the sources finished, look at the " \
-	      "results in $(BUILDDIR)/doctest/output.txt."
-
-xml: doc-requirements
-	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
-	@echo
-	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
-
-pseudoxml: doc-requirements
-	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
-	@echo
-	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)


=====================================
docs/conf.py
=====================================
@@ -1,9 +1,8 @@
-# -*- coding: utf-8 -*-
-#
 # This file is execfile()d with the current directory set to its containing dir.
 #
-# Note that not all possible configuration values are present in this
-# autogenerated file.
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
 #
 # All configuration values have a default; values that are commented out
 # serve to show the default.
@@ -13,15 +12,18 @@ import sys
 import inspect
 import shutil
 
-__location__ = os.path.join(os.getcwd(), os.path.dirname(
-    inspect.getfile(inspect.currentframe())))
+# -- Path setup --------------------------------------------------------------
+
+__location__ = os.path.join(
+    os.getcwd(), os.path.dirname(inspect.getfile(inspect.currentframe()))
+)
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-sys.path.insert(0, os.path.join(__location__, '../src'))
+sys.path.insert(0, os.path.join(__location__, "../src"))
 
-# -- Run sphinx-apidoc ------------------------------------------------------
+# -- Run sphinx-apidoc -------------------------------------------------------
 # This hack is necessary since RTD does not issue `sphinx-apidoc` before running
 # `sphinx-build -b html . _build/html`. See Issue:
 # https://github.com/rtfd/readthedocs.org/issues/1139
@@ -43,55 +45,65 @@ except FileNotFoundError:
 
 try:
     import sphinx
-    from pkg_resources import parse_version
 
-    cmd_line_template = "sphinx-apidoc -f -o {outputdir} {moduledir}"
+    cmd_line_template = (
+        "sphinx-apidoc --implicit-namespaces -f -o {outputdir} {moduledir}"
+    )
     cmd_line = cmd_line_template.format(outputdir=output_dir, moduledir=module_dir)
 
     args = cmd_line.split(" ")
-    if parse_version(sphinx.__version__) >= parse_version('1.7'):
+    if tuple(sphinx.__version__.split(".")) >= ("1", "7"):
+        # This is a rudimentary parse_version to avoid external dependencies
         args = args[1:]
 
     apidoc.main(args)
 except Exception as e:
     print("Running `sphinx-apidoc` failed!\n{}".format(e))
 
-# -- General configuration -----------------------------------------------------
+# -- General configuration ---------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
 # needs_sphinx = '1.0'
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.intersphinx', 'sphinx.ext.todo',
-              'sphinx.ext.autosummary', 'sphinx.ext.viewcode', 'sphinx.ext.coverage',
-              'sphinx.ext.doctest', 'sphinx.ext.ifconfig', 'sphinx.ext.mathjax',
-              'sphinx.ext.napoleon']
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.coverage",
+    "sphinx.ext.doctest",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.napoleon",
+]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix of source filenames.
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The encoding of source files.
 # source_encoding = 'utf-8-sig'
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = u'epimodels'
-copyright = u'2020, Flávio Codeço Coelho'
+project = "epimodels"
+copyright = "2021, Flávio Codeço Coelho"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = ''  # Is set by calling `setup.py docs`
+version = ""  # Is set by calling `setup.py docs`
 # The full version, including alpha/beta/rc tags.
-release = ''  # Is set by calling `setup.py docs`
+release = ""  # Is set by calling `setup.py docs`
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -105,7 +117,7 @@ release = ''  # Is set by calling `setup.py docs`
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = ['_build']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", ".venv"]
 
 # The reST default role (used for this markup: `text`) to use for all documents.
 # default_role = None
@@ -122,7 +134,7 @@ exclude_patterns = ['_build']
 # show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # A list of ignored prefixes for module index sorting.
 # modindex_common_prefix = []
@@ -131,18 +143,18 @@ pygments_style = 'sphinx'
 # keep_warnings = False
 
 
-# -- Options for HTML output ---------------------------------------------------
+# -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'alabaster'
+html_theme = "alabaster"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
 html_theme_options = {
-    'sidebar_width': '300px',
-    'page_width': '1200px'
+    "sidebar_width": "300px",
+    "page_width": "1200px"
 }
 
 # Add any paths that contain custom themes here, relative to this directory.
@@ -172,7 +184,7 @@ else:
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css"..
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
@@ -216,27 +228,24 @@ html_static_path = ['_static']
 # html_file_suffix = None
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'epimodels-doc'
+htmlhelp_basename = "epimodels-doc"
 
 
-# -- Options for LaTeX output --------------------------------------------------
+# -- Options for LaTeX output ------------------------------------------------
 
 latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-# 'papersize': 'letterpaper',
-
-# The font size ('10pt', '11pt' or '12pt').
-# 'pointsize': '10pt',
-
-# Additional stuff for the LaTeX preamble.
-# 'preamble': '',
+    # The paper size ("letterpaper" or "a4paper").
+    # "papersize": "letterpaper",
+    # The font size ("10pt", "11pt" or "12pt").
+    # "pointsize": "10pt",
+    # Additional stuff for the LaTeX preamble.
+    # "preamble": "",
 }
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-  ('index', 'user_guide.tex', u'epimodels Documentation',
-   u'Flávio Codeço Coelho', 'manual'),
+    ("index", "user_guide.tex", "epimodels Documentation", "Flávio Codeço Coelho", "manual")
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -259,14 +268,15 @@ latex_documents = [
 # If false, no module index is generated.
 # latex_domain_indices = True
 
-# -- External mapping ------------------------------------------------------------
-python_version = '.'.join(map(str, sys.version_info[0:2]))
+# -- External mapping --------------------------------------------------------
+python_version = ".".join(map(str, sys.version_info[0:2]))
 intersphinx_mapping = {
-    'sphinx': ('http://www.sphinx-doc.org/en/stable', None),
-    'python': ('https://docs.python.org/' + python_version, None),
-    'matplotlib': ('https://matplotlib.org', None),
-    'numpy': ('https://docs.scipy.org/doc/numpy', None),
-    'sklearn': ('http://scikit-learn.org/stable', None),
-    'pandas': ('http://pandas.pydata.org/pandas-docs/stable', None),
-    'scipy': ('https://docs.scipy.org/doc/scipy/reference', None),
+    "sphinx": ("http://www.sphinx-doc.org/en/stable", None),
+    "python": ("https://docs.python.org/" + python_version, None),
+    "matplotlib": ("https://matplotlib.org", None),
+    "numpy": ("https://docs.scipy.org/doc/numpy", None),
+    "sklearn": ("https://scikit-learn.org/stable", None),
+    "pandas": ("https://pandas.pydata.org/pandas-docs/stable", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/reference", None),
+    "pyscaffold": ("https://pyscaffold.org/en/stable", None),
 }


=====================================
requirements.txt
=====================================
@@ -1,17 +1,17 @@
-# =============================================================================
-# DEPRECATION WARNING:
-#
-# The file `requirements.txt` does not influence the package dependencies and
-# will not be automatically created in the next version of PyScaffold (v4.x).
-#
-# Please have look at the docs for better alternatives
-# (`Dependency Management` section).
-# =============================================================================
-#
 # Add your pinned requirements so that they can be easily installed with:
 # pip install -r requirements.txt
 # Remember to also add them in setup.cfg but unpinned.
 # Example:
 # numpy==1.13.3
 # scipy==1.0
-
+cython
+numpy
+scipy
+sympy
+pytest
+pytest-cov
+matplotlib
+mypy
+sphinx
+pyitlib
+numba


=====================================
setup.cfg
=====================================
@@ -20,14 +20,17 @@ classifiers =
 
 [options]
 zip_safe = False
-packages = find:
+packages = find_namespace:
 include_package_data = True
 package_dir =
     =src
 # DON'T CHANGE THE FOLLOWING LINE! IT WILL BE UPDATED BY PYSCAFFOLD!
-setup_requires = pyscaffold>=3.2a0,<3.3a0
 # Add here dependencies of your project (semicolon/line-separated), e.g.
-install_requires = numpy; scipy; cython
+install_requires =
+    importlib-metadata; python_version<"3.8"
+    numpy
+    scipy
+    cython
 # The usage of test_requires is discouraged, see `Dependency Management` docs
 # tests_require = pytest; pytest-cov
 # Require a specific Python version, e.g. Python 2.7 or >= 3.4
@@ -68,9 +71,9 @@ extras = True
 # Specify command line options as you would do when invoking py.test directly.
 # e.g. --cov-report html (or xml) for html/xml output or --junitxml junit.xml
 # in order to write a coverage file that can be read by Jenkins.
-addopts =
-    --cov epimodels --cov-report term-missing
-    --verbose
+#addopts =
+#    --cov epimodels --cov-report term-missing
+#    --verbose
 norecursedirs =
     dist
     build
@@ -78,8 +81,7 @@ norecursedirs =
 testpaths = tests
 
 [aliases]
-build = bdist_wheel
-release = build upload
+release = sdist bdist_wheel upload
 
 [bdist_wheel]
 # Use this option if your package is pure-python
@@ -93,7 +95,9 @@ build_dir = docs/_build
 # Options for the devpi: PyPI server and packaging tool
 # VCS export must be deactivated since we are using setuptools-scm
 no-vcs = 1
-formats = bdist_wheel
+formats =
+    sdist
+    bdist_wheel
 
 [flake8]
 # Some sane defaults for the code style checker flake8
@@ -107,5 +111,5 @@ exclude =
 [pyscaffold]
 # PyScaffold's parameters when the project was created.
 # This will be used when updating. Do not change!
-version = 3.2.3
+version = 4.0
 package = epimodels


=====================================
setup.py
=====================================
@@ -1,23 +1,21 @@
-# -*- coding: utf-8 -*-
 """
     Setup file for epimodels.
     Use setup.cfg to configure your project.
 
-    This file was generated with PyScaffold 3.2.3.
+    This file was generated with PyScaffold 4.0.
     PyScaffold helps you to put up the scaffold of your new Python project.
     Learn more under: https://pyscaffold.org/
 """
-import sys
-
-from pkg_resources import VersionConflict, require
 from setuptools import setup
 
-try:
-    require('setuptools>=38.3')
-except VersionConflict:
-    print("Error: version of setuptools is too old (<38.3)!")
-    sys.exit(1)
-
-
 if __name__ == "__main__":
-    setup(use_pyscaffold=True)
+    try:
+        setup(use_scm_version={"version_scheme": "no-guess-dev"})
+    except:  # noqa
+        print(
+            "\n\nAn error occurred while building the project, "
+            "please ensure you have the most updated version of setuptools, "
+            "setuptools_scm and wheel with:\n"
+            "   pip install -U setuptools setuptools_scm wheel\n\n"
+        )
+        raise


=====================================
src/epimodels/__init__.py
=====================================
@@ -1,23 +1,27 @@
-# -*- coding: utf-8 -*-
-from pkg_resources import get_distribution, DistributionNotFound
+import sys
+
+if sys.version_info[:2] >= (3, 8):
+    # TODO: Import directly (no need for conditional) when `python_requires = >= 3.8`
+    from importlib.metadata import PackageNotFoundError, version  # pragma: no cover
+else:
+    from importlib_metadata import PackageNotFoundError, version  # pragma: no cover
 
 try:
     # Change here if project is renamed and does not equal the package name
     dist_name = __name__
-    __version__ = get_distribution(dist_name).version
-except DistributionNotFound:
-    __version__ = 'unknown'
+    __version__ = version(dist_name)
+except PackageNotFoundError:  # pragma: no cover
+    __version__ = "unknown"
 finally:
-    del get_distribution, DistributionNotFound
+    del version, PackageNotFoundError
 
-from matplotlib import pyplot as P
 
+from matplotlib import pyplot as P
 
 class BaseModel:
     """
     Base class for all models both discrete and continuous
     """
-
     def __init__(self):
         self.name = None
         self.model_type = None
@@ -25,17 +29,14 @@ class BaseModel:
         self.parameters = {}
         self.traces = {}
 
-    def plot_traces(self, vars: list = []):
+    def plot_traces(self, vars: list=[]):
         """
         Plots the simulations
         :param vars: variables to plot
         """
-        if vars == []:  # Plot all
-            vars = [s for s in self.traces if s != 'time']
-
         for series, data in self.traces.items():
-            if series in vars:
+            if series in self.state_variables:
                 P.plot(self.traces['time'], data, label=series)
         P.legend(loc=0)
         P.grid()
-        P.title("{} model".format(self.model_type))
+        P.title("{} model".format(self.model_type))
\ No newline at end of file


=====================================
src/epimodels/tools/phase.py
=====================================
@@ -12,31 +12,31 @@ Created on 29/11/18
 by fccoelho
 license: GPL V3 or Later
 """
-import numpy
-from pyitlib import discrete_random_variable as drv
-import pylab as P
-
-class TimeDelayEmbedding:
-    def __init__(self, traces):
-        self.traces = traces
-
-    def mutual_information(self, data, tau_max=100):
-        mis = []
-
-        for tau in range(1, tau_max):
-            unlagged = data[:-tau]
-            lagged = numpy.roll(data, -tau)[:-tau]
-            joint = numpy.hstack((unlagged, lagged))
-            mis.append(drv.information_multi(joint))
-            if len(mis) > 1 and mis[-2] < mis[-1]:  # return first local minima
-                tau -= 1
-        return tau, mis
-
-    def _find_embedding_dimension(self, x, tau):
-        d = 2
-        while true:
-            ai = max([])
-
-    def show_mutual_information(self, mis):
-        P.plot(mis)
-        P.show()
+# import numpy
+# # from pyitlib import discrete_random_variable as drv
+# import pylab as P
+#
+# class TimeDelayEmbedding:
+#     def __init__(self, traces):
+#         self.traces = traces
+#
+#     def mutual_information(self, data, tau_max=100):
+#         mis = []
+#
+#         for tau in range(1, tau_max):
+#             unlagged = data[:-tau]
+#             lagged = numpy.roll(data, -tau)[:-tau]
+#             joint = numpy.hstack((unlagged, lagged))
+#             mis.append(drv.information_multi(joint))
+#             if len(mis) > 1 and mis[-2] < mis[-1]:  # return first local minima
+#                 tau -= 1
+#         return tau, mis
+#
+#     def _find_embedding_dimension(self, x, tau):
+#         d = 2
+#         while True:
+#             ai = max([])
+#
+#     def show_mutual_information(self, mis):
+#         P.plot(mis)
+#         P.show()



View it on GitLab: https://salsa.debian.org/med-team/python-epimodels/-/compare/376151a117cb1bbc9d184c615423f4da6384624b...8d5e96ce668393752d205a766306ccd46aad32ee

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-epimodels/-/compare/376151a117cb1bbc9d184c615423f4da6384624b...8d5e96ce668393752d205a766306ccd46aad32ee
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20210903/d90267b9/attachment-0001.htm>


More information about the debian-med-commit mailing list