From ce67f884ddfb7f2275ceda0263e035b8b01c519d Mon Sep 17 00:00:00 2001 From: joaoc Date: Wed, 28 Feb 2024 11:58:22 -0300 Subject: [PATCH 1/3] Update Python version and package dependencies --- python-package/.python-version | 1 + python-package/Makefile | 16 - python-package/README.md | 30 +- python-package/conda_requirements.txt | Bin 5304 -> 0 bytes python-package/geobr/list_geobr.py | 21 +- python-package/poetry.lock | 806 ++++++++++++++++++++++++++ python-package/pyproject.toml | 12 +- python-package/requirements-dev.txt | 9 - python-package/requirements.txt | 9 - 9 files changed, 829 insertions(+), 75 deletions(-) create mode 100644 python-package/.python-version delete mode 100644 python-package/Makefile delete mode 100644 python-package/conda_requirements.txt create mode 100644 python-package/poetry.lock delete mode 100644 python-package/requirements-dev.txt delete mode 100644 python-package/requirements.txt diff --git a/python-package/.python-version b/python-package/.python-version new file mode 100644 index 00000000..bd28b9c5 --- /dev/null +++ b/python-package/.python-version @@ -0,0 +1 @@ +3.9 diff --git a/python-package/Makefile b/python-package/Makefile deleted file mode 100644 index 5fa020a3..00000000 --- a/python-package/Makefile +++ /dev/null @@ -1,16 +0,0 @@ -build-env-dev: - python3 -m venv .venv; - . .venv/bin/activate; pip install -r requirements-dev.txt; - -update-env: - . .venv/bin/activate; pip install -r requirements-dev.txt; - -prepare-push: - black . - -publish: - @rm -rf dist - @rm -rf geobr.egg-info - @cp ../README.md master-README.md - @python setup.py sdist - @twine upload dist/* \ No newline at end of file diff --git a/python-package/README.md b/python-package/README.md index 5634f099..6e48ae65 100644 --- a/python-package/README.md +++ b/python-package/README.md @@ -11,13 +11,12 @@ To start the development environment run ```sh -make -. .venv/bin/activate +poetry install --no-root ``` Test with -`python -m pytest` +`poetry run pytest` You can use a helper to translate a function from R. If you want to add `read_biomes`, just run @@ -38,31 +37,6 @@ Before pushing, run `make prepare-push` -#### For Windows - -We recommend using conda and creating an environment that includes all libraries simultaneously. - -First create an environment and install Shapely and GDAL as such: - -`conda create --name geobr_env python=3.7` - -Activate the environmnet - -`conda activate geobr_env` - -Then add Shapely from conda-forge channel - `conda install shapely gdal -c conda-forge` - -Then the other packages -`conda install fiona pandas geopandas requests -c conda-forge` - -**Alternatively**, type on a terminal - -`conda create --name --file conda_requirements.txt` - -Finally, if **not** using conda, try: - -`pip install -r pip_requirements.txt` ## Translation Status diff --git a/python-package/conda_requirements.txt b/python-package/conda_requirements.txt deleted file mode 100644 index d3cfc55be7430b1c274e4391cf81b3b953204ec4..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 5304 zcmb7|*={076o%_MQr=;t z7XMKcJMnXW(sOt>x?Y8E;rH-cK;xf!myvEE?zX&}a3lI6%J>q#pC$hg9lvCZ-zC3| z{KrMdL6(4UDLqHY`X>IDh~y@W!XVNW!nO5vzi(1>(my(YL zW9tfk(@Sf4su2G|c~j~;`2)UW)C5~$+HSSB@^w#t8$OxaQ3W(xX|@lPw=Xv zm+*e>pC|F%opF!k`;;XE**jI-`_kOGpsK>FbP#3hK+jayYx#_&c9GP5Vwir83DTF8GreJ1;t!d1lxU}1IEhu0IrVMIrS7m_fOTw;;T z6H~jgmg2z@a)3%&pCi*3;=Z2DBn{i)p-T`YA_NlGmi-RrTu-T!iR>AD@Bw)`7bkHY zMvTo^mEtB&g+A@`>_Pmyj8#H)BEgZS&L+Y%iXNO?bh>uTH9TAB_;R#1)0PeO7~JK?@1i=R`g!WM(4&x2%U@V`bhDlD)HZ)dK+%fuASP?&QpgmmVvq+li9wVti&VXo`c0Y{M+u7zF$ zSzqbbp}3qs)-jhZW=%8a=$|v$wbifWjcH5C{}t+A>m1gRx;Pc!48ektaQBrX%p)wY z-J=?|>(xmebYy)c-ht3JZ6`12JuUTQt<`mSfrYs?(z@T<2P*EZdulKhdr>#=y3UiPSL4e|fzN!NsC~;i*=qTuDnQ4tr#!oMS&_r(}=5RfgqkckO-7O-HHIk7IoPiyj-%N6i0^^Rp>N zR$sHr9h%H{q^?of>W@8vZvN3)Q+sP?zgkD+g|hP|?ruz1tRO3R(|^fQ>TjxgTk1{4 zUPJP#P21e$h;xPPc0Y!L2~F-aC(XU`{!Q;*%ojQvwMqsY6i!R8Lsh8eChf<#=09MoFEqg-)eEpP&vx?EJ$n_FJ^HXODX%dqh8*% zew-7j7i15yfe>%1D#wx7outPn!o6^#iwd&0$;u=nVPlrEwXpN1%1;@bXqmR`-5qJ| zOJnBUTy}tuXYx!%)^ZBR9=ZbiZR!o}DtC^ZWR=e$^g{ejm-YTu$?l2nIq5UA6Nmpn z!XG&|T!(C($Xke${n9h!6wm9(_T)&k&3`*A-Mg-*0?`FOr`_f$J7IYiGHASOkaKMD z^i7bk!MT?`D?ZK|P#qOHP9Ga}VLX-iLB|e z$KGkqNq1{b;r!3j*Eg}RZ$B(4Ttq)}Hc3AI E7c<`PKmY&$ diff --git a/python-package/geobr/list_geobr.py b/python-package/geobr/list_geobr.py index 1f6d48b0..ceedb01b 100644 --- a/python-package/geobr/list_geobr.py +++ b/python-package/geobr/list_geobr.py @@ -1,23 +1,26 @@ from requests import get import pandas as pd +from io import StringIO from urllib.error import HTTPError def list_geobr(): - """ Prints available functions, according to latest README.md file + """Prints available functions, according to latest README.md file - Example output - ------------------------------ - Function: read_immediate_region - Geographies available: Immediate region - Years available: 2017 - Source: IBGE - ------------------------------ + Example output + ------------------------------ + Function: read_immediate_region + Geographies available: Immediate region + Years available: 2017 + Source: IBGE + ------------------------------ """ try: - df = pd.read_html(get("https://github.com/ipeaGIT/geobr/blob/master/README.md").text)[1] + html_data = get("https://github.com/ipeaGIT/geobr/blob/master/README.md").text + + df = pd.read_html(StringIO(html_data))[1] except HTTPError: print( diff --git a/python-package/poetry.lock b/python-package/poetry.lock new file mode 100644 index 00000000..51af082a --- /dev/null +++ b/python-package/poetry.lock @@ -0,0 +1,806 @@ +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. + +[[package]] +name = "atomicwrites" +version = "1.4.1" +description = "Atomic file writes." +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +files = [ + {file = "atomicwrites-1.4.1.tar.gz", hash = "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"}, +] + +[[package]] +name = "attrs" +version = "23.2.0" +description = "Classes Without Boilerplate" +optional = false +python-versions = ">=3.7" +files = [ + {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"}, + {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"}, +] + +[package.extras] +cov = ["attrs[tests]", "coverage[toml] (>=5.3)"] +dev = ["attrs[tests]", "pre-commit"] +docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"] +tests = ["attrs[tests-no-zope]", "zope-interface"] +tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"] +tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"] + +[[package]] +name = "certifi" +version = "2024.2.2" +description = "Python package for providing Mozilla's CA Bundle." +optional = false +python-versions = ">=3.6" +files = [ + {file = "certifi-2024.2.2-py3-none-any.whl", hash = "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1"}, + {file = "certifi-2024.2.2.tar.gz", hash = "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f"}, +] + +[[package]] +name = "charset-normalizer" +version = "3.3.2" +description = "The Real First Universal Charset Detector. 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Official Spatial Data Sets of Brazil" homepage = "https://github.com/ipeaGIT/geobr" @@ -19,11 +17,17 @@ packages = [ ] readme = "README.md" repository = "https://github.com/ipeaGIT/geobr" -version = "0.1.10-alpha.3" +version = "0.2.1" [tool.poetry.dependencies] -geopandas = "^0.7.0" +geopandas = "^0.14.0" shapely = "^1.7.0" +python = "^3.9" +requests = "^2.25.1" +lxml = "^5.1.0" + +[tool.poetry.dev-dependencies] +pytest = "^6.0" [tool.black] line-length = 88 diff --git a/python-package/requirements-dev.txt b/python-package/requirements-dev.txt deleted file mode 100644 index 45756800..00000000 --- a/python-package/requirements-dev.txt +++ /dev/null @@ -1,9 +0,0 @@ -geopandas==0.7.0 -jinja2>=2.11.3 -requests==2.20.0 -Shapely==1.7.0 -lxml -black -twine -pytest -fire \ No newline at end of file diff --git a/python-package/requirements.txt b/python-package/requirements.txt deleted file mode 100644 index c5e3d451..00000000 --- a/python-package/requirements.txt +++ /dev/null @@ -1,9 +0,0 @@ -geopandas==0.11.0 -jinja2>=2.11.3 -requests==2.20.0 -Shapely==1.8.1 -numpy>=1.22.4 -beautifulsoup4 -lxml -html5lib - From c451a51d13a7dacfdb7cc0cdb11188198b323dda Mon Sep 17 00:00:00 2001 From: joaoc Date: Wed, 28 Feb 2024 12:04:04 -0300 Subject: [PATCH 2/3] Add dependencies jinja2 and fire to dev-dependencies (closes update geopandas (python) #302) --- python-package/README.md | 11 ++- python-package/geobr/__init__.py | 3 +- python-package/poetry.lock | 116 ++++++++++++++++++++++- python-package/pyproject.toml | 2 + python-package/tests/test_read_biomes.py | 6 +- 5 files changed, 128 insertions(+), 10 deletions(-) diff --git a/python-package/README.md b/python-package/README.md index 6e48ae65..5515699a 100644 --- a/python-package/README.md +++ b/python-package/README.md @@ -11,7 +11,7 @@ To start the development environment run ```sh -poetry install --no-root +poetry install ``` Test with @@ -21,7 +21,10 @@ Test with You can use a helper to translate a function from R. If you want to add `read_biomes`, just run -`python helpers/translate_from_R.py read_biomes` +```sh +poetry shell +python helpers/translate_from_R.py read_biomes +``` It will scrape the original R function to get documentation and metadata. It adds: @@ -31,11 +34,9 @@ It adds: - larger documentation - very basic tests -! Be aware that if the function that you are adding is more complicated than the template. So, double always double check ! +! Be aware that if the function that you are adding is more complicated than the template. So, always double check ! -Before pushing, run -`make prepare-push` ## Translation Status diff --git a/python-package/geobr/__init__.py b/python-package/geobr/__init__.py index a424b273..e70d31e2 100644 --- a/python-package/geobr/__init__.py +++ b/python-package/geobr/__init__.py @@ -25,4 +25,5 @@ from .read_intermediate_region import read_intermediate_region from .read_urban_concentrations import read_urban_concentrations from .read_schools import read_schools -from .read_comparable_areas import read_comparable_areas \ No newline at end of file +from .read_comparable_areas import read_comparable_areas +from .read_biomes import read_biomes \ No newline at end of file diff --git a/python-package/poetry.lock b/python-package/poetry.lock index 51af082a..8996b180 100644 --- a/python-package/poetry.lock +++ b/python-package/poetry.lock @@ -247,6 +247,20 @@ calc = ["shapely"] s3 = ["boto3 (>=1.3.1)"] test = ["Fiona[s3]", "pytest (>=7)", "pytest-cov", "pytz"] +[[package]] +name = "fire" 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read_biomes(year=9999999) \ No newline at end of file From 2669a1a38873b2bfeae61dd2dbefde739bc3976e Mon Sep 17 00:00:00 2001 From: joaoc Date: Wed, 28 Feb 2024 12:16:35 -0300 Subject: [PATCH 3/3] Refactor Python-CMD-check.yaml to use Poetry for dependency management and update Python versions --- .github/workflows/Python-CMD-check.yaml | 46 +++++-------------------- 1 file changed, 9 insertions(+), 37 deletions(-) diff --git a/.github/workflows/Python-CMD-check.yaml b/.github/workflows/Python-CMD-check.yaml index b45a3fcd..56b273a7 100644 --- a/.github/workflows/Python-CMD-check.yaml +++ b/.github/workflows/Python-CMD-check.yaml @@ -25,8 +25,8 @@ jobs: strategy: fail-fast: false matrix: - os: [ubuntu-latest, macOS-latest , windows-latest] - python-version: ["3.8", "3.9", "3.10", "3.11"] + os: [ubuntu-latest, macOS-latest, windows-latest] + python-version: ["3.9", "3.10", "3.11"] # Python 3.8 support ends in 2024-10 # Python 3.12 support starts in 2023-10 # Check Python maintenance status at: https://www.python.org/downloads/ @@ -42,48 +42,20 @@ jobs: uses: actions/setup-python@v4 with: python-version: ${{ matrix.python-version }} - cache: 'pip' + cache: "pip" - - name: Install dependencies (Ubuntu) + - name: Install Poetry run: | python -m pip install --upgrade pip - pip install -r requirements.txt - # Add the Ubuntu GIS PPA - sudo add-apt-repository ppa:ubuntugis/ppa - sudo apt update - # Install geos library (shapely requirement) - sudo apt-get install libgeos++-dev libgeos3.10.2 libgeos-c1v5 libgeos-dev libgeos-doc - if: matrix.os == 'ubuntu-latest' - working-directory: python-package + pip install poetry - - name: Install dependencies (Windows) - run: | - python -m pip install --upgrade pip - pip install -r requirements.txt - if: matrix.os == 'windows-latest' - working-directory: python-package - - - name: Install dependencies (MacOS) - run: | - python -m pip install --upgrade pip - brew install geos - pip install shapely --no-binary shapely - pip install -r requirements.txt - if: matrix.os == 'macOS-latest' + - name: Install dependencies with Poetry + run: poetry install working-directory: python-package - - - name: Save dependencies - run: pip freeze > requirements.txt - - - name: Install testing dependencies - run: | - pip install pytest - pip install coverage - - name: Run tests + - name: Run tests with Poetry run: | - coverage run -m pytest -x ./tests - coverage report --omit="tests/*" -m >> test-results.txt + poetry run pytest ./tests working-directory: python-package - name: Upload check results