diff --git a/.github/workflows/lint-workflow.yml b/.github/workflows/lint-workflow.yml
index df4f4a8..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
@@ -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
- uses: actions/cache@v3
+ - name: Cache poetry
+ uses: actions/cache@v4
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..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
@@ -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
- uses: actions/cache@v3
+ - name: Cache poetry
+ uses: actions/cache@v4
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/.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/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 7d5c288..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
+ └── test_environment.py <- Helper script to test if environment is properly set
--------
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/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/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..bf89616 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",
@@ -33,14 +33,16 @@
"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",
"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\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",
@@ -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)"
]
},
{
@@ -527,7 +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",
@@ -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
},
diff --git a/poetry.lock b/poetry.lock
index e4f489f..d8f1c46 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 CLI commands via setuptools entry-points."
+optional = false
+python-versions = "*"
+files = [
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+]
+
+[package.dependencies]
+click = ">=4.0"
+
+[package.extras]
+dev = ["coveralls", "pytest (>=3.6)", "pytest-cov", "wheel"]
+
+[[package]]
+name = "cligj"
+version = "0.7.2"
+description = "Click params for commmand line interfaces to GeoJSON"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, <4"
+files = [
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+]
+
+[package.dependencies]
+click = ">=4.0"
+
+[package.extras]
+test = ["pytest-cov"]
+
[[package]]
name = "colorama"
version = "0.4.6"
@@ -507,6 +541,69 @@ traitlets = ">=4"
[package.extras]
test = ["pytest"]
+[[package]]
+name = "contourpy"
+version = "1.2.1"
+description = "Python library for calculating contours of 2D quadrilateral grids"
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+python-versions = ">=3.9"
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+[package.extras]
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+docs = ["furo", "sphinx (>=7.2)", "sphinx-copybutton"]
+mypy = ["contourpy[bokeh,docs]", "docutils-stubs", "mypy (==1.8.0)", "types-Pillow"]
+test = ["Pillow", "contourpy[test-no-images]", "matplotlib"]
+test-no-images = ["pytest", "pytest-cov", "pytest-xdist", "wurlitzer"]
+
[[package]]
name = "coverage"
version = "7.5.1"
@@ -571,6 +668,21 @@ files = [
[package.extras]
toml = ["tomli"]
+[[package]]
+name = "cycler"
+version = "0.12.1"
+description = "Composable style cycles"
+optional = false
+python-versions = ">=3.8"
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+tests = ["pytest", "pytest-cov", "pytest-xdist"]
+
[[package]]
name = "debugpy"
version = "1.8.1"
@@ -694,6 +806,53 @@ files = [
[package.extras]
devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benchmark", "pytest-cache", "validictory"]
+[[package]]
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+version = "1.9.6"
+description = "Fiona reads and writes spatial data files"
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+files = [
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+ {file = "widgetsnbextension-4.0.10.tar.gz", hash = "sha256:64196c5ff3b9a9183a8e699a4227fb0b7002f252c814098e66c4d1cd0644688f"},
+]
+
[metadata]
lock-version = "2.0"
python-versions = "~3.12"
-content-hash = "2c9a60c4287c497ced6f22659ca62ef3ac2df0ddb720fa18d295f99c51766708"
+content-hash = "db5f840e3feb0a3b19d892a0677564fbfb7a37a42550b9f28e41bd03d4d96887"
diff --git a/pyproject.toml b/pyproject.toml
index bff776e..46d02e0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -28,6 +28,12 @@ sphinx = "^7.3.7"
sphinx-rtd-theme = "^2.0.0"
sphinx-click = "^6.0.0"
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]
diff --git a/pytest.ini b/pytest.ini
index 749bd56..6320729 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -5,4 +5,5 @@ filterwarnings =
ignore:No uuidRepresentation is specified.*:DeprecationWarning
ignore:pkg_resources is deprecated as an API.*:DeprecationWarning
ignore:datetime.datetime.utcnow.*is deprecated and scheduled for removal in a future version.*:DeprecationWarning
- ignore: Country's official_name not found. 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
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 645ee24..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",
@@ -166,7 +165,7 @@ 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 +182,21 @@ 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)
+ country = 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
@@ -528,7 +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..491e738 100644
--- a/src/features/utils.py
+++ b/src/features/utils.py
@@ -12,10 +12,19 @@
import logging
import pathlib
import collections
+from typing import Tuple, List
+
+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,
@@ -171,7 +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.
@@ -185,7 +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.
"""
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