From cc765433298cde2b4c91b6fe113c20e0cc960f46 Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Thu, 23 May 2024 11:13:00 +0200 Subject: [PATCH 01/10] :construction_worker: attempt to configure poetry cache --- .github/workflows/lint-workflow.yml | 8 ++++---- .github/workflows/pytest-workflow.yml | 8 ++++---- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/.github/workflows/lint-workflow.yml b/.github/workflows/lint-workflow.yml index df4f4a8..03908ed 100644 --- a/.github/workflows/lint-workflow.yml +++ b/.github/workflows/lint-workflow.yml @@ -40,15 +40,15 @@ jobs: environment-file: conda-linux-64.lock use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly! - - name: Cache pip + - name: Cache poetry uses: actions/cache@v3 with: # This path is specific to Ubuntu - path: ~/.cache/pip + path: /.cache/pypoetry # Look to see if there is a cache hit for the corresponding requirements file - key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }} + key: ${{ runner.os }}-poetry-${{ hashFiles('poetry.lock') }} restore-keys: | - ${{ runner.os }}-pip- + ${{ runner.os }}-poetry- ${{ runner.os }}- - name: Conda info diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml index 485a724..876fd98 100644 --- a/.github/workflows/pytest-workflow.yml +++ b/.github/workflows/pytest-workflow.yml @@ -40,15 +40,15 @@ jobs: environment-file: conda-linux-64.lock use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly! - - name: Cache pip + - name: Cache poetry uses: actions/cache@v3 with: # This path is specific to Ubuntu - path: ~/.cache/pip + path: /.cache/pypoetry # Look to see if there is a cache hit for the corresponding requirements file - key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }} + key: ${{ runner.os }}-poetry-${{ hashFiles('poetry.lock') }} restore-keys: | - ${{ runner.os }}-pip- + ${{ runner.os }}-poetry- ${{ runner.os }}- - name: Conda info From 5525a91d8f915ffeaee4f1bf8812f83ec5bb8a67 Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Thu, 23 May 2024 11:16:00 +0200 Subject: [PATCH 02/10] :construction_worker: update actions dependencies --- .github/workflows/lint-workflow.yml | 6 +++--- .github/workflows/pytest-workflow.yml | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/lint-workflow.yml b/.github/workflows/lint-workflow.yml index 03908ed..8c2c754 100644 --- a/.github/workflows/lint-workflow.yml +++ b/.github/workflows/lint-workflow.yml @@ -18,10 +18,10 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Cache conda - uses: actions/cache@v3 + uses: actions/cache@v4 env: # Increase this value to reset cache if environment.yml has not changed CACHE_NUMBER: 0 @@ -41,7 +41,7 @@ jobs: use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly! - name: Cache poetry - uses: actions/cache@v3 + uses: actions/cache@v4 with: # This path is specific to Ubuntu path: /.cache/pypoetry diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml index 876fd98..3c3cc31 100644 --- a/.github/workflows/pytest-workflow.yml +++ b/.github/workflows/pytest-workflow.yml @@ -18,10 +18,10 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Cache conda - uses: actions/cache@v3 + uses: actions/cache@v4 env: # Increase this value to reset cache if environment.yml has not changed CACHE_NUMBER: 0 @@ -41,7 +41,7 @@ jobs: use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly! - name: Cache poetry - uses: actions/cache@v3 + uses: actions/cache@v4 with: # This path is specific to Ubuntu path: /.cache/pypoetry From af19ca4b675210663cf605ebb658dcb5b7aed946 Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Thu, 23 May 2024 11:31:46 +0200 Subject: [PATCH 03/10] :fire: drop tox configuration file --- README.md | 2 +- tox.ini | 41 ----------------------------------------- 2 files changed, 1 insertion(+), 42 deletions(-) delete mode 100644 tox.ini diff --git a/README.md b/README.md index 7d5c288..635edc5 100644 --- a/README.md +++ b/README.md @@ -61,7 +61,7 @@ Project Organization ├── requirements.txt <- The requirements file for reproducing the analysis environment, e.g. │ generated with `pip freeze > requirements.txt` ├── setup.py <- makes project pip installable (pip install -e .) so src can be imported - ├── test_environment.py <- Helper script to test if environment is properly set + └── test_environment.py <- Helper script to test if environment is properly set └── tox.ini <- Tox file with settings for running tox; see tox.readthedocs.io -------- diff --git a/tox.ini b/tox.ini deleted file mode 100644 index 705386f..0000000 --- a/tox.ini +++ /dev/null @@ -1,41 +0,0 @@ - -[tox] -envlist = clean,py39,flake8,report - -[flake8] -max-line-length = 79 -max-complexity = 10 -exclude = .ipynb_checkpoints - -[testenv:flake8] -basepython = python -deps = flake8 -commands = flake8 src - -[testenv:report] -deps = - coverage -skip_install = true -commands = - coverage report -m - coverage html - -[testenv:clean] -deps = coverage -skip_install = true -commands = coverage erase - -[testenv] -setenv = - PYTHONPATH = {toxinidir} -; passenv = -; TRAVIS -; TRAVIS_BRANCH -; TRAVIS_JOB_ID -deps = - -r{toxinidir}/requirements.txt -commands = - coverage run --append --source src -m pytest --basetemp={envtmpdir} -depends = - {py39}: clean - report: py39 From df8e8c2fd217b358af2a8d150f628649a713f17a Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Thu, 23 May 2024 11:32:51 +0200 Subject: [PATCH 04/10] :memo: update README --- HISTORY.rst | 2 +- README.md | 7 +++---- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/HISTORY.rst b/HISTORY.rst index c3834a3..a034ba2 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -12,11 +12,11 @@ TODO in database (which will be used as reference) * Map affymetrix snps in *OARV3* coordinates * Check if ``rs_id`` is still valid or not (with EVA) -* Manage python packages with `poetry `__ 0.4.10.dev0 ----------- +* Manage python packages with `poetry `__ (`#128 `__) * Add data for Guisandesa goats (`#117 `) * Rename ``manifacturer`` into ``manufacturer`` * Convert genotypes from *top* to *forward* (`#111 `__) diff --git a/README.md b/README.md index 635edc5..22b54fe 100644 --- a/README.md +++ b/README.md @@ -55,14 +55,13 @@ Project Organization ├── LICENSE <- Project LICENSE ├── Makefile <- Makefile with commands like `make data` or `make train` ├── README.md <- The top-level README for developers using this project. - ├── TODO.md <- Stuff that need to be done + ├── conda-linux-64.lock <- Conda environment lock file for linux 64 bit ├── environment.yml <- Conda environment file + ├── poetry.lock <- Poetry lock file + ├── pyproject.toml <- Poetry project file ├── pytest.ini <- Configuration file for `pytest` testing environment - ├── requirements.txt <- The requirements file for reproducing the analysis environment, e.g. - │ generated with `pip freeze > requirements.txt` ├── setup.py <- makes project pip installable (pip install -e .) so src can be imported └── test_environment.py <- Helper script to test if environment is properly set - └── tox.ini <- Tox file with settings for running tox; see tox.readthedocs.io -------- From d7dfa0795ccebc419d65a715e2cb807fac6d433f Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Thu, 23 May 2024 12:56:49 +0200 Subject: [PATCH 05/10] :recycle: refactor Country class --- .vscode/settings.json | 1 + src/features/smarterdb.py | 16 +++++++++------- 2 files changed, 10 insertions(+), 7 deletions(-) diff --git a/.vscode/settings.json b/.vscode/settings.json index 572d8bd..c039777 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -22,6 +22,7 @@ "pedfile", "plinkio", "probeset", + "pycountry", "SGID", "smarterdb", "SNPCHIMP", diff --git a/src/features/smarterdb.py b/src/features/smarterdb.py index 645ee24..2134442 100644 --- a/src/features/smarterdb.py +++ b/src/features/smarterdb.py @@ -166,7 +166,7 @@ class Country(mongoengine.Document): """The country numeric code""" official_name = mongoengine.StringField() - """Country ufficial name""" + """Country official name""" species = mongoengine.ListField(mongoengine.StringField()) """The sample species find within this country""" @@ -183,19 +183,21 @@ def __init__(self, name: str = None, *args, **kwargs): kwargs["species"] = [kwargs["species"]] # initialize base object - super(Country, self).__init__(*args, **kwargs) + super(Country, self).__init__(*args, name=name, **kwargs) + + if not self.id and name: + logger.warning(f"Creating country object for '{name}'") - if name: # get a country object if name.lower() == "unknown": country = UnknownCountry() else: country = pycountry.countries.get(name=name) - self.alpha_2 = country.alpha_2 - self.alpha_3 = country.alpha_3 - self.name = name - self.numeric = country.numeric + if country: + self.alpha_2 = country.alpha_2 + self.alpha_3 = country.alpha_3 + self.numeric = country.numeric if hasattr(country, "official_name"): self.official_name = country.official_name From f99ed86f830b91fefc44aceb8f20b6a3cf8496a4 Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Thu, 23 May 2024 12:58:04 +0200 Subject: [PATCH 06/10] :heavy_plus_sign: add missing dependencies --- poetry.lock | 606 ++++++++++++++++++++++++++++++++++++++++++++++++- pyproject.toml | 3 + pytest.ini | 3 +- 3 files changed, 610 insertions(+), 2 deletions(-) diff --git a/poetry.lock b/poetry.lock index e4f489f..3b451b9 100644 --- a/poetry.lock +++ b/poetry.lock @@ -479,6 +479,40 @@ docs = ["Pallets-Sphinx-Themes", "m2r2", "sphinx"] tests = ["pytest"] tests-cov = ["coverage", "coveralls", "pytest", "pytest-cov"] +[[package]] +name = "click-plugins" +version = "1.1.1" +description = "An extension module for click to enable registering 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Country name provided instead.*:UserWarning + ignore:Country.s official_name not found. Country name provided instead.*:UserWarning + ignore:Deprecated call to .pkg_resources.declare_namespace.'sphinxcontrib'.*:DeprecationWarning From a6afa9749539a429c2da15e10f2cc94c93326d41 Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Thu, 23 May 2024 13:06:31 +0200 Subject: [PATCH 07/10] :monocle_face: update notebooks --- .../exploratory/0.26.0-bunop-guisandesa.ipynb | 10 +++--- .../results/0.2.0-bunop-smarter_summary.ipynb | 32 ++++++++----------- .../results/0.3.0-bunop-sheep_metadata.ipynb | 4 +-- .../results/0.3.1-bunop-goat_metadata.ipynb | 4 +-- 4 files changed, 23 insertions(+), 27 deletions(-) diff --git a/notebooks/exploratory/0.26.0-bunop-guisandesa.ipynb b/notebooks/exploratory/0.26.0-bunop-guisandesa.ipynb index 55b2ced..c8d97c2 100644 --- a/notebooks/exploratory/0.26.0-bunop-guisandesa.ipynb +++ b/notebooks/exploratory/0.26.0-bunop-guisandesa.ipynb @@ -146,7 +146,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "a952d068174a41319b80040d02534b4c", + "model_id": "12c36628beb54c40a1312ac74d24e3c9", "version_major": 2, "version_minor": 0 }, @@ -187,7 +187,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "2b1dd34bbb6948bbb896b9d7558f7bfc", + "model_id": "be208ae027924004a9c2dcec31626854", "version_major": 2, "version_minor": 0 }, @@ -331,7 +331,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -345,9 +345,9 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.1" + "version": "3.12.3" } }, "nbformat": 4, - "nbformat_minor": 2 + "nbformat_minor": 4 } diff --git a/notebooks/results/0.2.0-bunop-smarter_summary.ipynb b/notebooks/results/0.2.0-bunop-smarter_summary.ipynb index 9291314..f41c631 100644 --- a/notebooks/results/0.2.0-bunop-smarter_summary.ipynb +++ b/notebooks/results/0.2.0-bunop-smarter_summary.ipynb @@ -5,7 +5,7 @@ "id": "3cc84f47-db82-43eb-99fd-78768ecd2a99", "metadata": {}, "source": [ - "# SMARTER SUMMARY (2024/03/01)\n", + "# SMARTER SUMMARY (2024/05/23)\n", "* [Dataset composition](#datasets-composition)\n", " * [Foreground / background datasets](#foreground-vs-background-datasets)\n", " * [Datasets by chip type](#datasets-by-chip-type)\n", @@ -33,6 +33,8 @@ "source": [ "import json\n", "from collections import defaultdict\n", + "from io import StringIO\n", + "\n", "import pandas as pd\n", "import matplotlib.pyplot as plt\n", "from shapely.geometry import Point\n", @@ -40,7 +42,7 @@ "import pycountry\n", "from mpl_toolkits.axes_grid1 import make_axes_locatable\n", "\n", - "from src.features.smarterdb import global_connection, Dataset, SampleSheep, SampleGoat\n", + "from src.features.smarterdb import global_connection, Dataset, SampleSheep, SampleGoat, Country\n", "\n", "conn = global_connection()\n", "\n", @@ -227,9 +229,9 @@ "metadata": {}, "outputs": [], "source": [ - "tmp = foreground_sheep.to_json()\n", + "tmp = StringIO(foreground_sheep.to_json())\n", "foreground_sheep = pd.read_json(tmp).dropna(axis=0)\n", - "tmp = background_sheep.to_json()\n", + "tmp = StringIO(background_sheep.to_json())\n", "background_sheep = pd.read_json(tmp).dropna(axis=0)\n", "\n", "foreground_sheep = fix_id(foreground_sheep)\n", @@ -357,9 +359,9 @@ "metadata": {}, "outputs": [], "source": [ - "tmp = foreground_goats.to_json()\n", + "tmp = StringIO(foreground_goats.to_json())\n", "foreground_goats = pd.read_json(tmp).dropna(thresh=1, axis=1)\n", - "tmp = background_goats.to_json()\n", + "tmp = StringIO(background_goats.to_json())\n", "background_goats = pd.read_json(tmp).dropna(thresh=1, axis=1)\n", "\n", "foreground_goats = fix_id(foreground_goats)\n", @@ -506,7 +508,7 @@ "all_sheep = pd.concat([foreground_sheep, background_sheep], axis=0)\n", "sheep_by_country = all_sheep.value_counts('country')\n", "sheep_by_country = pd.DataFrame(data=sheep_by_country, columns=['count']).reset_index()\n", - "sheep_by_country['iso_a3'] = sheep_by_country['country'].apply(lambda country: pycountry.countries.search_fuzzy(country)[0].alpha_3)" + "sheep_by_country['iso_a3'] = sheep_by_country['country'].apply(lambda country: Country.objects.get(name=country).alpha_3)" ] }, { @@ -586,7 +588,7 @@ "all_goats = pd.concat([foreground_goats, background_goats], axis=0)\n", "goats_by_country = all_goats.value_counts('country')\n", "goats_by_country = pd.DataFrame(data=goats_by_country, columns=['count']).reset_index()\n", - "goats_by_country['iso_a3'] = goats_by_country['country'].apply(lambda country: pycountry.countries.search_fuzzy(country)[0].alpha_3)" + "goats_by_country['iso_a3'] = goats_by_country['country'].apply(lambda country: Country.objects.get(name=country).alpha_3)" ] }, { @@ -642,7 +644,7 @@ "source": [ "sheep_breeds_by_country = all_sheep[[\"country\", \"breed\"]].drop_duplicates().reset_index(drop=True).value_counts(\"country\")\n", "sheep_breeds_by_country = pd.DataFrame(data=sheep_breeds_by_country, columns=['count']).reset_index()\n", - "sheep_breeds_by_country['iso_a3'] = sheep_breeds_by_country['country'].apply(lambda country: pycountry.countries.search_fuzzy(country)[0].alpha_3)\n", + "sheep_breeds_by_country['iso_a3'] = sheep_breeds_by_country['country'].apply(lambda country: Country.objects.get(name=country).alpha_3)\n", "sheep_breeds_by_country = pd.merge(sheep_breeds_by_country, world, how=\"outer\", on='iso_a3')[['country', 'iso_a3', 'continent', 'geometry', 'count']]\n", "sheep_breeds_by_country = gpd.GeoDataFrame(sheep_breeds_by_country)" ] @@ -687,7 +689,7 @@ "source": [ "goat_breeds_by_country = all_goats[[\"country\", \"breed\"]].drop_duplicates().reset_index(drop=True).value_counts(\"country\")\n", "goat_breeds_by_country = pd.DataFrame(data=goat_breeds_by_country, columns=['count']).reset_index()\n", - "goat_breeds_by_country['iso_a3'] = goat_breeds_by_country['country'].apply(lambda country: pycountry.countries.search_fuzzy(country)[0].alpha_3)\n", + "goat_breeds_by_country['iso_a3'] = goat_breeds_by_country['country'].apply(lambda country: Country.objects.get(name=country).alpha_3)\n", "goat_breeds_by_country = pd.merge(goat_breeds_by_country, world, how=\"outer\", on='iso_a3')[['country', 'iso_a3', 'continent', 'geometry', 'count']]\n", "goat_breeds_by_country = gpd.GeoDataFrame(goat_breeds_by_country)" ] @@ -712,17 +714,11 @@ "plt.savefig('goat-breeds-by-country.png', dpi=300, bbox_inches='tight')\n", "plt.show()" ] - }, - { - "cell_type": "markdown", - "id": "50445a3b", - "metadata": {}, - "source": [] } ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -736,7 +732,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.1" + "version": "3.12.3" } }, "nbformat": 4, diff --git a/notebooks/results/0.3.0-bunop-sheep_metadata.ipynb b/notebooks/results/0.3.0-bunop-sheep_metadata.ipynb index fd9e062..8de3d9b 100644 --- a/notebooks/results/0.3.0-bunop-sheep_metadata.ipynb +++ b/notebooks/results/0.3.0-bunop-sheep_metadata.ipynb @@ -316,7 +316,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -330,7 +330,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.1" + "version": "3.12.3" }, "toc-showtags": false }, diff --git a/notebooks/results/0.3.1-bunop-goat_metadata.ipynb b/notebooks/results/0.3.1-bunop-goat_metadata.ipynb index e26b146..3ec3691 100644 --- a/notebooks/results/0.3.1-bunop-goat_metadata.ipynb +++ b/notebooks/results/0.3.1-bunop-goat_metadata.ipynb @@ -319,7 +319,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -333,7 +333,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.1" + "version": "3.12.3" }, "toc-showtags": false }, From 95138b13afe604be37369065dba98c8f3fcd17bb Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Thu, 23 May 2024 13:12:27 +0200 Subject: [PATCH 08/10] :heavy_plus_sign: add missing dependencies --- docs/getting-started.rst | 2 +- poetry.lock | 92 +++++++++++++++++++++++++++++++++++++++- pyproject.toml | 3 ++ 3 files changed, 95 insertions(+), 2 deletions(-) diff --git a/docs/getting-started.rst b/docs/getting-started.rst index 5d68f9a..1f245c6 100644 --- a/docs/getting-started.rst +++ b/docs/getting-started.rst @@ -59,7 +59,7 @@ SMARTER-database requirements *SMARTER-database* is managed through a `conda `__ environment, in which python executable and other non-python dependencies are specified. Moreover, python dependencies are -managed through a ``requirements.txt`` file. Dependencies and environment set up +managed using `poetry `__. Dependencies and environment set up is managed through the GNU linux ``make`` command. The MongoDB instance of this project is managed by `docker `__ and `docker-compose `__, however you can configure an environment variable to set up a connection with diff --git a/poetry.lock b/poetry.lock index 3b451b9..d8f1c46 100644 --- a/poetry.lock +++ b/poetry.lock @@ -945,6 +945,17 @@ files = [ {file = "fqdn-1.5.1.tar.gz", hash = "sha256:105ed3677e767fb5ca086a0c1f4bb66ebc3c100be518f0e0d755d9eae164d89f"}, ] +[[package]] +name = "geographiclib" +version = "2.0" +description = "The geodesic routines from GeographicLib" +optional = false +python-versions = ">=3.7" +files = [ + {file = "geographiclib-2.0-py3-none-any.whl", hash = "sha256:6b7225248e45ff7edcee32becc4e0a1504c606ac5ee163a5656d482e0cd38734"}, + {file = "geographiclib-2.0.tar.gz", hash = "sha256:f7f41c85dc3e1c2d3d935ec86660dc3b2c848c83e17f9a9e51ba9d5146a15859"}, +] + [[package]] name = "geopandas" version = "0.14.4" @@ -964,6 +975,29 @@ pandas = ">=1.4.0" pyproj = ">=3.3.0" shapely = ">=1.8.0" +[[package]] +name = "geopy" +version = "2.4.1" +description = "Python Geocoding Toolbox" +optional = false +python-versions = ">=3.7" +files = [ + {file = "geopy-2.4.1-py3-none-any.whl", hash = "sha256:ae8b4bc5c1131820f4d75fce9d4aaaca0c85189b3aa5d64c3dcaf5e3b7b882a7"}, + {file = "geopy-2.4.1.tar.gz", hash = "sha256:50283d8e7ad07d89be5cb027338c6365a32044df3ae2556ad3f52f4840b3d0d1"}, +] + +[package.dependencies] +geographiclib = ">=1.52,<3" + +[package.extras] +aiohttp = ["aiohttp"] +dev = ["coverage", "flake8 (>=5.0,<5.1)", "isort (>=5.10.0,<5.11.0)", "pytest (>=3.10)", "pytest-asyncio (>=0.17)", "readme-renderer", "sphinx (<=4.3.2)", "sphinx-issues", "sphinx-rtd-theme (>=0.5.0)"] +dev-docs = ["readme-renderer", "sphinx (<=4.3.2)", "sphinx-issues", "sphinx-rtd-theme (>=0.5.0)"] +dev-lint = ["flake8 (>=5.0,<5.1)", "isort (>=5.10.0,<5.11.0)"] +dev-test = ["coverage", "pytest (>=3.10)", "pytest-asyncio (>=0.17)", "sphinx (<=4.3.2)"] +requests = ["requests (>=2.16.2)", "urllib3 (>=1.24.2)"] +timezone = ["pytz"] + [[package]] name = "h11" version = "0.14.0" @@ -1122,6 +1156,27 @@ qtconsole = ["qtconsole"] test = ["pickleshare", "pytest", "pytest-asyncio (<0.22)", "testpath"] test-extra = ["curio", "ipython[test]", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.23)", "pandas", "trio"] +[[package]] +name = "ipywidgets" +version = "8.1.2" +description = "Jupyter interactive widgets" +optional = false +python-versions = ">=3.7" +files = [ + {file = "ipywidgets-8.1.2-py3-none-any.whl", hash = "sha256:bbe43850d79fb5e906b14801d6c01402857996864d1e5b6fa62dd2ee35559f60"}, + {file = "ipywidgets-8.1.2.tar.gz", hash = "sha256:d0b9b41e49bae926a866e613a39b0f0097745d2b9f1f3dd406641b4a57ec42c9"}, +] + +[package.dependencies] +comm = ">=0.1.3" +ipython = ">=6.1.0" +jupyterlab-widgets = ">=3.0.10,<3.1.0" +traitlets = ">=4.3.1" +widgetsnbextension = ">=4.0.10,<4.1.0" + +[package.extras] +test = ["ipykernel", "jsonschema", "pytest (>=3.6.0)", "pytest-cov", "pytz"] + [[package]] name = "isoduration" version = "20.11.0" @@ -1441,6 +1496,17 @@ docs = ["autodoc-traits", "jinja2 (<3.2.0)", "mistune (<4)", "myst-parser", "pyd openapi = ["openapi-core (>=0.18.0,<0.19.0)", "ruamel-yaml"] test = ["hatch", "ipykernel", "openapi-core (>=0.18.0,<0.19.0)", "openapi-spec-validator (>=0.6.0,<0.8.0)", "pytest (>=7.0,<8)", "pytest-console-scripts", "pytest-cov", "pytest-jupyter[server] (>=0.6.2)", "pytest-timeout", "requests-mock", "ruamel-yaml", "sphinxcontrib-spelling", "strict-rfc3339", "werkzeug"] +[[package]] +name = "jupyterlab-widgets" +version = "3.0.10" +description = "Jupyter interactive widgets for JupyterLab" +optional = false +python-versions = ">=3.7" +files = [ + {file = "jupyterlab_widgets-3.0.10-py3-none-any.whl", hash = "sha256:dd61f3ae7a5a7f80299e14585ce6cf3d6925a96c9103c978eda293197730cb64"}, + {file = "jupyterlab_widgets-3.0.10.tar.gz", hash = "sha256:04f2ac04976727e4f9d0fa91cdc2f1ab860f965e504c29dbd6a65c882c9d04c0"}, +] + [[package]] name = "kiwisolver" version = "1.4.5" @@ -2442,6 +2508,19 @@ files = [ {file = "pycparser-2.22.tar.gz", hash = "sha256:491c8be9c040f5390f5bf44a5b07752bd07f56edf992381b05c701439eec10f6"}, ] +[[package]] +name = "pyensemblrest" +version = "0.2.3" +description = "An easy way to access EnsEMBL data with Python." +optional = false +python-versions = "*" +files = [ + {file = "pyensemblrest-0.2.3.tar.gz", hash = "sha256:a547bb7c6c45ac0466f82e18831652c378ba16a1a0efc85781ff14c1b058be9e"}, +] + +[package.dependencies] +requests = ">=1.0.0" + [[package]] name = "pyflakes" version = "3.2.0" @@ -3561,7 +3640,18 @@ docs = ["Sphinx (>=6.0)", "myst-parser (>=2.0.0)", "sphinx-rtd-theme (>=1.1.0)"] optional = ["python-socks", "wsaccel"] test = ["websockets"] +[[package]] +name = "widgetsnbextension" +version = "4.0.10" +description = "Jupyter interactive widgets for Jupyter Notebook" +optional = false +python-versions = ">=3.7" +files = [ + {file = "widgetsnbextension-4.0.10-py3-none-any.whl", hash = "sha256:d37c3724ec32d8c48400a435ecfa7d3e259995201fbefa37163124a9fcb393cc"}, + {file = "widgetsnbextension-4.0.10.tar.gz", hash = "sha256:64196c5ff3b9a9183a8e699a4227fb0b7002f252c814098e66c4d1cd0644688f"}, +] + [metadata] lock-version = "2.0" python-versions = "~3.12" -content-hash = "8c6d68d4c56d64812d7db765d61af0067f3f9588bbb6ac950eb4c27e34d67c6b" +content-hash = "db5f840e3feb0a3b19d892a0677564fbfb7a37a42550b9f28e41bd03d4d96887" diff --git a/pyproject.toml b/pyproject.toml index 9b935bd..46d02e0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -31,6 +31,9 @@ autodocsumm = "^0.2.12" matplotlib = "^3.9.0" shapely = "^2.0.4" geopandas = "^0.14.4" +pyensemblrest = "^0.2.3" +ipywidgets = "^8.1.2" +geopy = "^2.4.1" [build-system] From c96349eb1f2393f72c5f5a6bf8ed5eee2b12bd3a Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Thu, 23 May 2024 15:38:24 +0200 Subject: [PATCH 09/10] :recycle: deal again with pycountry track turkey in a custom pycountry instance and using the custom instance when searching countries --- ...-bunop-reverse_geocoding-ovine_SNP50.ipynb | 10 ++-- ...22.0-bunop-new_sheep_background_data.ipynb | 56 +++++++++++-------- .../results/0.2.0-bunop-smarter_summary.ipynb | 4 +- src/data/import_breeds.py | 2 + src/data/import_samples.py | 5 +- src/features/smarterdb.py | 7 +-- src/features/utils.py | 6 ++ 7 files changed, 53 insertions(+), 37 deletions(-) diff --git a/notebooks/exploratory/0.10.1-bunop-reverse_geocoding-ovine_SNP50.ipynb b/notebooks/exploratory/0.10.1-bunop-reverse_geocoding-ovine_SNP50.ipynb index b76694c..3ab7841 100644 --- a/notebooks/exploratory/0.10.1-bunop-reverse_geocoding-ovine_SNP50.ipynb +++ b/notebooks/exploratory/0.10.1-bunop-reverse_geocoding-ovine_SNP50.ipynb @@ -17,12 +17,12 @@ "outputs": [], "source": [ "import pandas as pd\n", - "import pycountry\n", "\n", "from geopy.geocoders import Nominatim\n", "from geopy.extra.rate_limiter import RateLimiter\n", "from tqdm.notebook import tqdm\n", "\n", + "from src.features.utils import countries\n", "from src.features.smarterdb import global_connection, Dataset" ] }, @@ -216,7 +216,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "d8df7ad85ccf44cd99f825483c245887", + "model_id": "c2cdae511e6b4e5dabf5f3a432398697", "version_major": 2, "version_minor": 0 }, @@ -235,7 +235,7 @@ " data = rgeocode(coordinate, language=\"English\")\n", " if data:\n", " country_code = data.raw['address']['country_code']\n", - " return pycountry.countries.get(alpha_2=country_code).name\n", + " return countries.get(alpha_2=country_code).name\n", " else:\n", " return data\n", "infos[\"country\"] = infos[\"coordinates\"].progress_apply(get_country)" @@ -569,7 +569,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -583,7 +583,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.1" + "version": "3.12.3" } }, "nbformat": 4, diff --git a/notebooks/exploratory/0.22.0-bunop-new_sheep_background_data.ipynb b/notebooks/exploratory/0.22.0-bunop-new_sheep_background_data.ipynb index e52f5f3..3b2e451 100644 --- a/notebooks/exploratory/0.22.0-bunop-new_sheep_background_data.ipynb +++ b/notebooks/exploratory/0.22.0-bunop-new_sheep_background_data.ipynb @@ -28,7 +28,6 @@ "\n", "import numpy as np\n", "import pandas as pd\n", - "import pycountry\n", "from tqdm.notebook import tqdm\n", "from geopy.geocoders import Nominatim\n", "from geopy.extra.rate_limiter import RateLimiter\n", @@ -37,6 +36,7 @@ "\n", "from src.features.smarterdb import global_connection, Dataset, SampleSheep\n", "from src.features.plinkio import TextPlinkIO, BinaryPlinkIO, CodingException\n", + "from src.features.utils import countries\n", "from src.data.common import WORKING_ASSEMBLIES, AssemblyConf" ] }, @@ -220,7 +220,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "d8c53a08951644bc9dbbaa2e99016978", + "model_id": "9dc3f0261f4f4e28979cc0069b65cc8f", "version_major": 2, "version_minor": 0 }, @@ -264,7 +264,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Got {'Llanwenog', 'Balwen', 'TregaronWelshMountain', 'Llawenog', 'TalybontWelshMountain', 'SouthWalesWelshMountain', 'Lleyn', 'LlandoveryWhiteFaced', 'DolgellauWelshMountain', 'ClunForest', 'WelshMountainHillFlock', 'BrecknockHillCheviot', 'HillRadnor', 'BadgerFaced', 'ImprovedWelshMountain', 'Beulah', 'KerryHill', 'HardySpeckledFaced', 'BlackWelshMountain'} breeds\n" + "Got {'Llanwenog', 'Beulah', 'Balwen', 'Lleyn', 'BadgerFaced', 'TregaronWelshMountain', 'WelshMountainHillFlock', 'ImprovedWelshMountain', 'KerryHill', 'ClunForest', 'HardySpeckledFaced', 'DolgellauWelshMountain', 'SouthWalesWelshMountain', 'LlandoveryWhiteFaced', 'TalybontWelshMountain', 'Llawenog', 'BlackWelshMountain', 'BrecknockHillCheviot', 'HillRadnor'} breeds\n" ] } ], @@ -310,7 +310,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "{'Llanwenog': 'Llanwenog', 'Balwen': 'Balwen', 'TregaronWelshMountain': 'Tregaron Welsh Mountain', 'Llawenog': 'Llawenog', 'TalybontWelshMountain': 'Talybont Welsh Mountain', 'SouthWalesWelshMountain': 'South Wales Welsh Mountain', 'Lleyn': 'Lleyn', 'LlandoveryWhiteFaced': 'Llandovery White Faced', 'DolgellauWelshMountain': 'Dolgellau Welsh Mountain', 'ClunForest': 'Clun Forest', 'WelshMountainHillFlock': 'Welsh Mountain Hill Flock', 'BrecknockHillCheviot': 'Brecknock Hill Cheviot', 'HillRadnor': 'Hill Radnor', 'BadgerFaced': 'Badger Faced', 'ImprovedWelshMountain': 'Improved Welsh Mountain', 'Beulah': 'Beulah', 'KerryHill': 'Kerry Hill', 'HardySpeckledFaced': 'Hardy Speckled Faced', 'BlackWelshMountain': 'Black Welsh Mountain'}\n" + "{'Llanwenog': 'Llanwenog', 'Beulah': 'Beulah', 'Balwen': 'Balwen', 'Lleyn': 'Lleyn', 'BadgerFaced': 'Badger Faced', 'TregaronWelshMountain': 'Tregaron Welsh Mountain', 'WelshMountainHillFlock': 'Welsh Mountain Hill Flock', 'ImprovedWelshMountain': 'Improved Welsh Mountain', 'KerryHill': 'Kerry Hill', 'ClunForest': 'Clun Forest', 'HardySpeckledFaced': 'Hardy Speckled Faced', 'DolgellauWelshMountain': 'Dolgellau Welsh Mountain', 'SouthWalesWelshMountain': 'South Wales Welsh Mountain', 'LlandoveryWhiteFaced': 'Llandovery White Faced', 'TalybontWelshMountain': 'Talybont Welsh Mountain', 'Llawenog': 'Llawenog', 'BlackWelshMountain': 'Black Welsh Mountain', 'BrecknockHillCheviot': 'Brecknock Hill Cheviot', 'HillRadnor': 'Hill Radnor'}\n" ] } ], @@ -469,7 +469,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "c47e48b6f4d947708be1fdbad12e34f0", + "model_id": "7b3512fc33c84582bf02223c7988bd43", "version_major": 2, "version_minor": 0 }, @@ -528,7 +528,7 @@ " 7 Ho 8 non-null float64\n", " 8 Ho (SD) 8 non-null float64\n", "dtypes: float64(4), int64(1), object(4)\n", - "memory usage: 704.0+ bytes\n" + "memory usage: 708.0+ bytes\n" ] } ], @@ -1668,7 +1668,7 @@ " 7 Source 16 non-null object \n", " 8 Ho 16 non-null float64\n", "dtypes: float64(3), int64(2), object(4)\n", - "memory usage: 1.2+ KB\n" + "memory usage: 1.3+ KB\n" ] } ], @@ -2498,7 +2498,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "c77eb62bceae401083f1e2b3e062d264", + "model_id": "ad74d746c63a4d829b674d9994b94477", "version_major": 2, "version_minor": 0 }, @@ -2900,7 +2900,7 @@ "output_type": "stream", "text": [ "\n", - "Int64Index: 910 entries, 0 to 909\n", + "RangeIndex: 910 entries, 0 to 909\n", "Data columns (total 20 columns):\n", " # Column Non-Null Count Dtype \n", "--- ------ -------------- ----- \n", @@ -2925,7 +2925,7 @@ " 18 country_old 910 non-null object \n", " 19 region_old 856 non-null object \n", "dtypes: float64(7), int64(1), object(12)\n", - "memory usage: 149.3+ KB\n" + "memory usage: 142.3+ KB\n" ] } ], @@ -3099,18 +3099,19 @@ { "data": { "text/plain": [ + "breed\n", "Croatian Isles 90\n", - "Gentile di Puglia 24\n", - "Bergamasca 24\n", - "Massese 24\n", + "Norwegian White 24\n", "Xisqueta 24\n", + "Sardinian mouflon 24\n", + "Zel 24\n", " ..\n", - "Dalmatian 4\n", "Schoonebeker 4\n", + "Sumavska 4\n", "Recka 2\n", - "Dubska 2\n", "Privorska 2\n", - "Name: breed, Length: 61, dtype: int64" + "Dubska 2\n", + "Name: count, Length: 61, dtype: int64" ] }, "execution_count": 49, @@ -3139,10 +3140,11 @@ { "data": { "text/plain": [ + "breed\n", "Sardinian mouflon 24\n", "European mouflon 21\n", "Iranian mouflon 14\n", - "Name: breed, dtype: int64" + "Name: count, dtype: int64" ] }, "execution_count": 50, @@ -3610,7 +3612,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "0bbde783cce047268ce5a825f40390a7", + "model_id": "5be71ec1425a4826a26d5c0cf32d3c02", "version_major": 2, "version_minor": 0 }, @@ -4090,7 +4092,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "ebac2f58b31f4a678a1b56dfb6bf3e73", + "model_id": "93f177b8cbdb461487a74860ece64daa", "version_major": 2, "version_minor": 0 }, @@ -4258,7 +4260,7 @@ " data = rgeocode(coordinate, language=\"English\")\n", " if data:\n", " country_code = data.raw['address']['country_code']\n", - " return pycountry.countries.get(alpha_2=country_code).name\n", + " return countries.get(alpha_2=country_code).name\n", " else:\n", " return data\n", "\n", @@ -4788,7 +4790,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "46f9b1f0b5e541f3b320a0fba510b53f", + "model_id": "5bbd4402a08b4a56a8565e309549eb39", "version_major": 2, "version_minor": 0 }, @@ -4966,6 +4968,14 @@ "id": "2b340aaf-5749-4f2e-ba54-348c185e5313", "metadata": {}, "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/tmp/ipykernel_165225/3722076925.py:1: FutureWarning: DataFrame.fillna with 'method' is deprecated and will raise in a future version. Use obj.ffill() or obj.bfill() instead.\n", + " gaouar_2017_sheeps.fillna(method='ffill', axis=0, inplace=True)\n" + ] + }, { "data": { "text/html": [ @@ -6546,7 +6556,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -6560,7 +6570,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.1" + "version": "3.12.3" } }, "nbformat": 4, diff --git a/notebooks/results/0.2.0-bunop-smarter_summary.ipynb b/notebooks/results/0.2.0-bunop-smarter_summary.ipynb index f41c631..bf89616 100644 --- a/notebooks/results/0.2.0-bunop-smarter_summary.ipynb +++ b/notebooks/results/0.2.0-bunop-smarter_summary.ipynb @@ -39,10 +39,10 @@ "import matplotlib.pyplot as plt\n", "from shapely.geometry import Point\n", "import geopandas as gpd\n", - "import pycountry\n", "from mpl_toolkits.axes_grid1 import make_axes_locatable\n", "\n", "from src.features.smarterdb import global_connection, Dataset, SampleSheep, SampleGoat, Country\n", + "from src.features.utils import countries\n", "\n", "conn = global_connection()\n", "\n", @@ -529,7 +529,7 @@ "def fix_iso_a3(name, iso_a3):\n", " if iso_a3 == '-99':\n", " try:\n", - " return pycountry.countries.search_fuzzy(name.split()[-1])[0].alpha_3\n", + " return countries.search_fuzzy(name.split()[-1])[0].alpha_3\n", " except LookupError:\n", " return \"-99\"\n", " else:\n", diff --git a/src/data/import_breeds.py b/src/data/import_breeds.py index 7ab64b6..450e6af 100644 --- a/src/data/import_breeds.py +++ b/src/data/import_breeds.py @@ -102,6 +102,8 @@ def main(species_class, src_dataset, dst_dataset, datafile, code_column, # dealing with original file alias = BreedAlias(fid=fid, dataset=dst_dataset, country=country) + logger.debug(f"Got alias: {alias}") + try: breed, modified = get_or_create_breed( species_class=species_class.capitalize(), diff --git a/src/data/import_samples.py b/src/data/import_samples.py index 0765a6a..dba6d1e 100644 --- a/src/data/import_samples.py +++ b/src/data/import_samples.py @@ -22,7 +22,6 @@ MutuallyExclusiveOptionGroup) from mongoengine.errors import DoesNotExist -import pycountry from pandas.core.series import Series from src.data.common import ( @@ -31,7 +30,7 @@ from src.features.smarterdb import ( global_connection, Breed, get_or_create_sample, get_sample_type, SmarterDBException) -from src.features.utils import UnknownCountry +from src.features.utils import UnknownCountry, countries logger = logging.getLogger(__name__) @@ -53,7 +52,7 @@ def find_country(country: str): return UnknownCountry() # transform country string with pycountry - fuzzy = pycountry.countries.search_fuzzy(country)[0] + fuzzy = countries.search_fuzzy(country)[0] logger.info(f"Found {fuzzy} for {country}") diff --git a/src/features/smarterdb.py b/src/features/smarterdb.py index 2134442..db78e8c 100644 --- a/src/features/smarterdb.py +++ b/src/features/smarterdb.py @@ -9,7 +9,6 @@ import os import logging import pathlib -import pycountry import mongoengine from enum import Enum @@ -18,7 +17,7 @@ from pymongo import database, ReturnDocument, MongoClient from dotenv import find_dotenv, load_dotenv -from .utils import get_project_dir, UnknownCountry +from .utils import get_project_dir, UnknownCountry, countries SPECIES2CODE = { "Sheep": "OA", @@ -192,7 +191,7 @@ def __init__(self, name: str = None, *args, **kwargs): if name.lower() == "unknown": country = UnknownCountry() else: - country = pycountry.countries.get(name=name) + country = countries.get(name=name) if country: self.alpha_2 = country.alpha_2 @@ -530,7 +529,7 @@ def getSmarterId( if country.lower() == "unknown": country = UnknownCountry() else: - country = pycountry.countries.get(name=country) + country = countries.get(name=country) # get two letter code for country country_code = country.alpha_2 diff --git a/src/features/utils.py b/src/features/utils.py index f6de455..bb70be6 100644 --- a/src/features/utils.py +++ b/src/features/utils.py @@ -13,9 +13,15 @@ import pathlib import collections +from pycountry import countries + # Get an instance of a logger logger = logging.getLogger(__name__) +# manage custom countries +# english name for turkey +countries.add_entry(alpha_2="TR", alpha_3="TUR", name="Turkey", numeric="792", official_name='Republic of Türkiye') + def sanitize( word: str, From 339c1e194cb259d62c0d0a43bdad8f849f9341d8 Mon Sep 17 00:00:00 2001 From: Paolo Cozzi Date: Thu, 23 May 2024 15:44:34 +0200 Subject: [PATCH 10/10] :rotating_light: fix issues with flake --- src/features/utils.py | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/src/features/utils.py b/src/features/utils.py index bb70be6..491e738 100644 --- a/src/features/utils.py +++ b/src/features/utils.py @@ -12,6 +12,7 @@ import logging import pathlib import collections +from typing import Tuple, List from pycountry import countries @@ -20,7 +21,9 @@ # manage custom countries # english name for turkey -countries.add_entry(alpha_2="TR", alpha_3="TUR", name="Turkey", numeric="792", official_name='Republic of Türkiye') +countries.add_entry( + alpha_2="TR", alpha_3="TUR", name="Turkey", numeric="792", + official_name='Republic of Türkiye') def sanitize( @@ -177,7 +180,8 @@ def find_duplicates(header: list) -> list: return to_remove -def skip_comments(handle: io.TextIOWrapper, comment_char="#") -> (int, list): +def skip_comments( + handle: io.TextIOWrapper, comment_char="#") -> Tuple[int, List[str]]: """ Ignore comments lines from a open file handle. Return the stream position immediately after the comments and all the comment lines in a list. @@ -191,7 +195,7 @@ def skip_comments(handle: io.TextIOWrapper, comment_char="#") -> (int, list): Returns ------- - (int, list) + Tuple[int, List[str]] The stream position after the comments and the ignored lines as a list. """