From 8a0ff35a3f3723c9ced3bac100f761b8efe88080 Mon Sep 17 00:00:00 2001 From: Matthew Archer Date: Tue, 10 Jan 2023 18:45:25 +0000 Subject: [PATCH 01/17] initial commit of python2 deployment ci --- .github/workflows/python-app.yaml | 40 +++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 .github/workflows/python-app.yaml diff --git a/.github/workflows/python-app.yaml b/.github/workflows/python-app.yaml new file mode 100644 index 00000000..e91f9648 --- /dev/null +++ b/.github/workflows/python-app.yaml @@ -0,0 +1,40 @@ +# This workflow will install Python dependencies, run tests and lint with a single version of Python +# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python + +name: Python application + +on: + push: + branches: [ "main" ] + pull_request: + branches: [ "main" ] + +permissions: + contents: read + +jobs: + build: + + # 20.04 currently still supports old version of python (ubuntu-latest doesn't) + runs-on: ubuntu-20.04 + + steps: + - uses: actions/checkout@v3 + - name: Set up Python 2.7.10 + uses: actions/setup-python@v3 + with: + python-version: "2.7.10" + - 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 From 3c07bc5e240ebe9a42545ddc358d8a036dda7cc1 Mon Sep 17 00:00:00 2001 From: Matthew Archer Date: Tue, 10 Jan 2023 18:46:50 +0000 Subject: [PATCH 02/17] syntax fix --- .github/workflows/python-app.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python-app.yaml b/.github/workflows/python-app.yaml index e91f9648..cfce1c5d 100644 --- a/.github/workflows/python-app.yaml +++ b/.github/workflows/python-app.yaml @@ -15,7 +15,7 @@ permissions: jobs: build: - # 20.04 currently still supports old version of python (ubuntu-latest doesn't) + # 20.04 currently still supports old version of python (ubuntu-latest doesn't) runs-on: ubuntu-20.04 steps: From fb670c89523bf8b649f07c85daf21fdecf7a2ac4 Mon Sep 17 00:00:00 2001 From: Matthew Archer Date: Tue, 10 Jan 2023 18:49:48 +0000 Subject: [PATCH 03/17] syntax fix --- .github/workflows/python-app.yaml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.github/workflows/python-app.yaml b/.github/workflows/python-app.yaml index cfce1c5d..2c30a65e 100644 --- a/.github/workflows/python-app.yaml +++ b/.github/workflows/python-app.yaml @@ -14,10 +14,7 @@ permissions: jobs: build: - - # 20.04 currently still supports old version of python (ubuntu-latest doesn't) runs-on: ubuntu-20.04 - steps: - uses: actions/checkout@v3 - name: Set up Python 2.7.10 From 3d3aa88d0829204c8cf3c262078f7f7450ae32a4 Mon Sep 17 00:00:00 2001 From: Matthew Archer Date: Tue, 10 Jan 2023 18:52:25 +0000 Subject: [PATCH 04/17] change branch --- .github/workflows/python-app.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/python-app.yaml b/.github/workflows/python-app.yaml index 2c30a65e..40d7a49e 100644 --- a/.github/workflows/python-app.yaml +++ b/.github/workflows/python-app.yaml @@ -5,9 +5,9 @@ name: Python application on: push: - branches: [ "main" ] + branches: [ "ci" ] pull_request: - branches: [ "main" ] + branches: [ "ci" ] permissions: contents: read From 5703c1fccb58eea84bd90a80e0278a7a909046e2 Mon Sep 17 00:00:00 2001 From: Matthew Archer Date: Tue, 10 Jan 2023 18:53:41 +0000 Subject: [PATCH 05/17] change python version --- .github/workflows/python-app.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/python-app.yaml b/.github/workflows/python-app.yaml index 40d7a49e..e09f8231 100644 --- a/.github/workflows/python-app.yaml +++ b/.github/workflows/python-app.yaml @@ -17,10 +17,10 @@ jobs: runs-on: ubuntu-20.04 steps: - uses: actions/checkout@v3 - - name: Set up Python 2.7.10 + - name: Set up Python 2.7.18 uses: actions/setup-python@v3 with: - python-version: "2.7.10" + python-version: "2.7.18" - name: Install dependencies run: | python -m pip install --upgrade pip From eb9d91813dc7a096af05df46db6f0a70f41cc60c Mon Sep 17 00:00:00 2001 From: Matthew Archer Date: Wed, 11 Jan 2023 11:58:33 +0000 Subject: [PATCH 06/17] added simple partitioning_nt test run and pytest example --- .github/workflows/python-app.yaml | 24 +++++++++++-- frozen-requirements.txt | 14 ++++++++ oneflux/tools/partition_nt.py | 56 +++++++++++++++++++++++++++++++ oneflux_steps/Makefile | 2 +- 4 files changed, 93 insertions(+), 3 deletions(-) create mode 100644 frozen-requirements.txt diff --git a/.github/workflows/python-app.yaml b/.github/workflows/python-app.yaml index e09f8231..b079628a 100644 --- a/.github/workflows/python-app.yaml +++ b/.github/workflows/python-app.yaml @@ -21,11 +21,31 @@ jobs: uses: actions/setup-python@v3 with: python-version: "2.7.18" - - name: Install dependencies + - name: Install OneFLUX run: | python -m pip install --upgrade pip pip install flake8 pytest - if [ -f requirements.txt ]; then pip install -r requirements.txt; fi + # if [ -f requirements-frozen.txt ]; then pip install -r requirements-frozen.txt; fi + make + - name: Run OneFLUX partitioning_nt + run: | + # get necessary data + wget ftp://ftp.fluxdata.org/.ameriflux_downloads/.test/US-ARc_sample_input.zip + wget ftp://ftp.fluxdata.org/.ameriflux_downloads/.test/US-ARc_sample_output.zip + unzip US-ARc_sample_input.zip -d ./datadir/test_input/ + unzip US-ARc_sample_output.zip -d ./datadir/test_output/ + # copy necessary output data to force partitioning_nt to run + cp -r ./datadir/test_output/US-ARc_sample_output/02_qc_auto/ ./datadir/test_input/US-ARc_sample_input/ + cp -r ./datadir/test_output/US-ARc_sample_output/07_meteo_proc/ ./datadir/test_input/US-ARc_sample_input/ + cp -r ./datadir/test_output/US-ARc_sample_output/08_nee_proc/ ./datadir/test_input/US-ARc_sample_input/ + python runoneflux.py partition_nt ./datadir/test_input/ US-ARc US-ARc_sample_input 2005 2006 -l fluxnet_pipeline_US-ARc.log --recint hh + + - name: Run pytest + run: | + pytest oneflux/tools/partition_nt.py + + + # - name: Lint with flake8 # run: | # # stop the build if there are Python syntax errors or undefined names diff --git a/frozen-requirements.txt b/frozen-requirements.txt new file mode 100644 index 00000000..af23b1fa --- /dev/null +++ b/frozen-requirements.txt @@ -0,0 +1,14 @@ +backports.functools-lru-cache==1.6.4 +cycler==0.10.0 +kiwisolver==1.1.0 +matplotlib==2.2.5 +numpy==1.15.4 +pandas==0.20.0 +patsy==0.5.2 +pyparsing==2.4.7 +python-dateutil==2.8.2 +pytz==2022.4 +scipy==1.2.3 +six==1.16.0 +statsmodels==0.8.0 +subprocess32==3.5.4 diff --git a/oneflux/tools/partition_nt.py b/oneflux/tools/partition_nt.py index 92034b8d..3e8ce31c 100644 --- a/oneflux/tools/partition_nt.py +++ b/oneflux/tools/partition_nt.py @@ -12,6 +12,7 @@ ''' import sys import os +import glob import logging import time import numpy @@ -19,6 +20,7 @@ import socket import numpy import calendar +import pytest from datetime import datetime from io import StringIO @@ -133,6 +135,60 @@ def run_partition_nt(datadir, siteid, sitedir, years_to_compare, remove_previous_run(datadir=datadir, siteid=siteid, sitedir=sitedir, python=py_remove_old, prod_to_compare=prod_to_compare, perc_to_compare=perc_to_compare, years_to_compare=years_to_compare) run_python(datadir=datadir, siteid=siteid, sitedir=sitedir, prod_to_compare=prod_to_compare, perc_to_compare=perc_to_compare, years_to_compare=years_to_compare) +@pytest.fixture +def get_data(): + pass + +def equal_csv(csv_1, csv_2): + with open(csv_1, 'r') as t1, open(csv_2, 'r') as t2: + fileone = t1.readlines() + filetwo = t2.readlines() + for line in filetwo: + if line not in fileone: + return False + +# deal with fixtures for running nt_test +# step 10 +def test_run_partition_nt(): + + datadir = "../datadir/" + siteid = "US-ARc" + sitedir = "US-ARc_sample_input" + years = [2005] # years = [2005, 2006] + PROD_TO_COMPARE = ['c', 'y'] + # PERC_TO_COMPARE = ['1.25', '3.75',] + PERC_TO_COMPARE = ['1.25',] + remove_previous_run(datadir=datadir, siteid=siteid, sitedir=sitedir, python=True, + prod_to_compare=PROD_TO_COMPARE, perc_to_compare=PERC_TO_COMPARE, + years_to_compare=years) + + run_python(datadir=datadir, siteid=siteid, sitedir=sitedir, prod_to_compare=PROD_TO_COMPARE, + perc_to_compare=PERC_TO_COMPARE, years_to_compare=years) + + # now do simple check of output + rootdir = os.path.join(datadir, sitedir, "10_nee_partition_nt") + nee_y_files = glob.glob(os.path.join(rootdir, "nee_y_1.25_US-ARc_2005*")) + compare_y_files = glob.glob(os.path.join('saved', "nee_y_1.25_US-ARc_2005*")) + + # log.info(nee_y_files) + # log.info(compare_y_files) + for f, b in zip(nee_y_files, compare_y_files): + if not equal_csv(f, b): + return False + + # glob the files with this root + # for file in glob.glob(nee_y_files): + # print(file) + # log.info(file) + # if not equal_csv(file, ) + + + + + + # with open('saved/nee_y_1.25_US-ARc_2005.csv', 'r') as t1, open(nee_y, 'r') as t2: + + if __name__ == '__main__': raise ONEFluxError('Not executable') diff --git a/oneflux_steps/Makefile b/oneflux_steps/Makefile index d56115bf..a5e22cc9 100644 --- a/oneflux_steps/Makefile +++ b/oneflux_steps/Makefile @@ -31,7 +31,7 @@ CC := gcc -O3 MKDIR = mkdir -p # copy file command (verbose, keep file metadata) -COPY = cp -av +COPY = cp -v SRCDIR := $(shell pwd)/ TGTDIR := ${HOME}/bin/oneflux/ From 4e1f5876c105812d61f39ffa3d8f714a9922ca07 Mon Sep 17 00:00:00 2001 From: Matthew Archer Date: Wed, 11 Jan 2023 12:03:08 +0000 Subject: [PATCH 07/17] updated build to point to frozen requirements --- .github/workflows/python-app.yaml | 2 +- Makefile | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/python-app.yaml b/.github/workflows/python-app.yaml index b079628a..6ea4379b 100644 --- a/.github/workflows/python-app.yaml +++ b/.github/workflows/python-app.yaml @@ -25,7 +25,7 @@ jobs: run: | python -m pip install --upgrade pip pip install flake8 pytest - # if [ -f requirements-frozen.txt ]; then pip install -r requirements-frozen.txt; fi + # if [ -f frozen-requirement.txt ]; then pip install -r frozen-requirements.txt; fi make - name: Run OneFLUX partitioning_nt run: | diff --git a/Makefile b/Makefile index 58665241..4d258567 100644 --- a/Makefile +++ b/Makefile @@ -6,7 +6,7 @@ buildpy: @echo "Installing Python dependencies..." ifeq ($(PYPACKAGE),pip) @echo "Using pip to install dependencies..." - pip install -r requirements.txt + pip install -r frozen-requirements.txt else ifeq ($(PYPACKAGE),conda) @echo "Using conda to install dependencies..." From 03318a5a9110e4476b8764e86091d89ebf108527 Mon Sep 17 00:00:00 2001 From: Matthew Archer Date: Wed, 11 Jan 2023 14:06:00 +0000 Subject: [PATCH 08/17] removed software health tools --- .github/workflows/python-app.yaml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/.github/workflows/python-app.yaml b/.github/workflows/python-app.yaml index 6ea4379b..7d92bf0b 100644 --- a/.github/workflows/python-app.yaml +++ b/.github/workflows/python-app.yaml @@ -23,17 +23,21 @@ jobs: python-version: "2.7.18" - name: Install OneFLUX run: | - python -m pip install --upgrade pip - pip install flake8 pytest + # python -m pip install --upgrade pip + # pip install flake8 pytest # if [ -f frozen-requirement.txt ]; then pip install -r frozen-requirements.txt; fi make - - name: Run OneFLUX partitioning_nt + -name: Get data run: | + mkdir datadir # get necessary data wget ftp://ftp.fluxdata.org/.ameriflux_downloads/.test/US-ARc_sample_input.zip wget ftp://ftp.fluxdata.org/.ameriflux_downloads/.test/US-ARc_sample_output.zip unzip US-ARc_sample_input.zip -d ./datadir/test_input/ unzip US-ARc_sample_output.zip -d ./datadir/test_output/ + + - name: Run OneFLUX partitioning_nt + run: | # copy necessary output data to force partitioning_nt to run cp -r ./datadir/test_output/US-ARc_sample_output/02_qc_auto/ ./datadir/test_input/US-ARc_sample_input/ cp -r ./datadir/test_output/US-ARc_sample_output/07_meteo_proc/ ./datadir/test_input/US-ARc_sample_input/ From 53d948b44edba159468b83cc3f81d528764c7b39 Mon Sep 17 00:00:00 2001 From: Matthew Archer Date: Wed, 11 Jan 2023 14:07:20 +0000 Subject: [PATCH 09/17] fix syntax --- .github/workflows/python-app.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python-app.yaml b/.github/workflows/python-app.yaml index 7d92bf0b..b4003efe 100644 --- a/.github/workflows/python-app.yaml +++ b/.github/workflows/python-app.yaml @@ -27,7 +27,7 @@ jobs: # pip install flake8 pytest # if [ -f frozen-requirement.txt ]; then pip install -r frozen-requirements.txt; fi make - -name: Get data + - name: Get data run: | mkdir datadir # get necessary data From 79b88d8241a32d74faf465354fc86fc0e6724d10 Mon Sep 17 00:00:00 2001 From: Matthew Archer Date: Wed, 11 Jan 2023 14:11:44 +0000 Subject: [PATCH 10/17] add setuptools to frozen-requirements.txt --- frozen-requirements.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/frozen-requirements.txt b/frozen-requirements.txt index af23b1fa..6280a83b 100644 --- a/frozen-requirements.txt +++ b/frozen-requirements.txt @@ -12,3 +12,4 @@ scipy==1.2.3 six==1.16.0 statsmodels==0.8.0 subprocess32==3.5.4 +setuptools==44.1.1 From 2e1e23cd3203996ce77f7c65062789cf988d33d3 Mon Sep 17 00:00:00 2001 From: Matthew Archer Date: Wed, 11 Jan 2023 14:13:45 +0000 Subject: [PATCH 11/17] upgrade pip --- .github/workflows/python-app.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/python-app.yaml b/.github/workflows/python-app.yaml index b4003efe..b40bcffe 100644 --- a/.github/workflows/python-app.yaml +++ b/.github/workflows/python-app.yaml @@ -23,7 +23,8 @@ jobs: python-version: "2.7.18" - name: Install OneFLUX run: | - # python -m pip install --upgrade pip + python -m pip install --upgrade pip + pip install setuptools==44.1.1 # pip install flake8 pytest # if [ -f frozen-requirement.txt ]; then pip install -r frozen-requirements.txt; fi make From 4ea607b98a645f695f2bfb88fe633cc2c925d8ab Mon Sep 17 00:00:00 2001 From: Matthew Archer Date: Wed, 11 Jan 2023 14:18:36 +0000 Subject: [PATCH 12/17] add wheel to prevent source build of pandas --- .github/workflows/python-app.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python-app.yaml b/.github/workflows/python-app.yaml index b40bcffe..e0db1c2f 100644 --- a/.github/workflows/python-app.yaml +++ b/.github/workflows/python-app.yaml @@ -24,7 +24,7 @@ jobs: - name: Install OneFLUX run: | python -m pip install --upgrade pip - pip install setuptools==44.1.1 + pip install setuptools==44.1.1 wheel # pip install flake8 pytest # if [ -f frozen-requirement.txt ]; then pip install -r frozen-requirements.txt; fi make From fc5e796d11a522d802cefafe955429dd64694659 Mon Sep 17 00:00:00 2001 From: Matthew Archer Date: Wed, 11 Jan 2023 14:24:32 +0000 Subject: [PATCH 13/17] try forcing pandas wheel collection --- frozen-requirements.txt | 1 - 1 file changed, 1 deletion(-) diff --git a/frozen-requirements.txt b/frozen-requirements.txt index 6280a83b..e4c5b7b5 100644 --- a/frozen-requirements.txt +++ b/frozen-requirements.txt @@ -2,7 +2,6 @@ backports.functools-lru-cache==1.6.4 cycler==0.10.0 kiwisolver==1.1.0 matplotlib==2.2.5 -numpy==1.15.4 pandas==0.20.0 patsy==0.5.2 pyparsing==2.4.7 From ea44b8b034d586cafaae08ca761ed1e152dd09c1 Mon Sep 17 00:00:00 2001 From: Matthew Archer Date: Wed, 11 Jan 2023 14:39:45 +0000 Subject: [PATCH 14/17] add pytest and bump pandas --- .github/workflows/python-app.yaml | 2 +- frozen-requirements.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/python-app.yaml b/.github/workflows/python-app.yaml index e0db1c2f..7bd47a52 100644 --- a/.github/workflows/python-app.yaml +++ b/.github/workflows/python-app.yaml @@ -24,7 +24,7 @@ jobs: - name: Install OneFLUX run: | python -m pip install --upgrade pip - pip install setuptools==44.1.1 wheel + pip install setuptools==44.1.1 wheel pytest # pip install flake8 pytest # if [ -f frozen-requirement.txt ]; then pip install -r frozen-requirements.txt; fi make diff --git a/frozen-requirements.txt b/frozen-requirements.txt index e4c5b7b5..d92e10cb 100644 --- a/frozen-requirements.txt +++ b/frozen-requirements.txt @@ -2,7 +2,7 @@ backports.functools-lru-cache==1.6.4 cycler==0.10.0 kiwisolver==1.1.0 matplotlib==2.2.5 -pandas==0.20.0 +pandas==0.20.1 patsy==0.5.2 pyparsing==2.4.7 python-dateutil==2.8.2 From 0030188f9e104f6a63a34b502741eba18fdcc2e8 Mon Sep 17 00:00:00 2001 From: Matthew Archer Date: Wed, 11 Jan 2023 14:45:54 +0000 Subject: [PATCH 15/17] attempt with old build system --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index 4d258567..58665241 100644 --- a/Makefile +++ b/Makefile @@ -6,7 +6,7 @@ buildpy: @echo "Installing Python dependencies..." ifeq ($(PYPACKAGE),pip) @echo "Using pip to install dependencies..." - pip install -r frozen-requirements.txt + pip install -r requirements.txt else ifeq ($(PYPACKAGE),conda) @echo "Using conda to install dependencies..." From e15d25c158dc32e4a886224c8452b695e075d376 Mon Sep 17 00:00:00 2001 From: Matthew Archer Date: Wed, 11 Jan 2023 15:20:16 +0000 Subject: [PATCH 16/17] amend pytest example --- Makefile | 2 +- oneflux/tools/partition_nt.py | 16 ++++++---------- pytest.ini | 5 +++++ 3 files changed, 12 insertions(+), 11 deletions(-) create mode 100644 pytest.ini diff --git a/Makefile b/Makefile index 58665241..4d258567 100644 --- a/Makefile +++ b/Makefile @@ -6,7 +6,7 @@ buildpy: @echo "Installing Python dependencies..." ifeq ($(PYPACKAGE),pip) @echo "Using pip to install dependencies..." - pip install -r requirements.txt + pip install -r frozen-requirements.txt else ifeq ($(PYPACKAGE),conda) @echo "Using conda to install dependencies..." diff --git a/oneflux/tools/partition_nt.py b/oneflux/tools/partition_nt.py index 3e8ce31c..60240df2 100644 --- a/oneflux/tools/partition_nt.py +++ b/oneflux/tools/partition_nt.py @@ -147,11 +147,11 @@ def equal_csv(csv_1, csv_2): if line not in fileone: return False -# deal with fixtures for running nt_test +# TODO: deal with fixtures for running nt_test # step 10 def test_run_partition_nt(): - - datadir = "../datadir/" + datadir = "./datadir/test_input" + data_output = "./datadir/test_output" siteid = "US-ARc" sitedir = "US-ARc_sample_input" years = [2005] # years = [2005, 2006] @@ -168,11 +168,12 @@ def test_run_partition_nt(): # now do simple check of output rootdir = os.path.join(datadir, sitedir, "10_nee_partition_nt") nee_y_files = glob.glob(os.path.join(rootdir, "nee_y_1.25_US-ARc_2005*")) - compare_y_files = glob.glob(os.path.join('saved', "nee_y_1.25_US-ARc_2005*")) + ref_output = os.path.join(data_output, sitedir, "10_nee_partition_nt") + ref_y_files = glob.glob(os.path.join(ref_output, "nee_y_1.25_US-ARc_2005*")) # log.info(nee_y_files) # log.info(compare_y_files) - for f, b in zip(nee_y_files, compare_y_files): + for f, b in zip(nee_y_files, ref_y_files): if not equal_csv(f, b): return False @@ -181,11 +182,6 @@ def test_run_partition_nt(): # print(file) # log.info(file) # if not equal_csv(file, ) - - - - - # with open('saved/nee_y_1.25_US-ARc_2005.csv', 'r') as t1, open(nee_y, 'r') as t2: diff --git a/pytest.ini b/pytest.ini new file mode 100644 index 00000000..f5276a23 --- /dev/null +++ b/pytest.ini @@ -0,0 +1,5 @@ +[pytest] +log_cli = 1 +log_cli_level = INFO +log_cli_format = %(asctime)s [%(levelname)8s] %(message)s (%(filename)s:%(lineno)s) +log_cli_date_format=%Y-%m-%d %H:%M:%S From 7667c936ce6aa0104deaf14d04a7204e24f261a7 Mon Sep 17 00:00:00 2001 From: Matthew Archer Date: Wed, 11 Jan 2023 15:28:49 +0000 Subject: [PATCH 17/17] remove whitespace --- .github/workflows/python-app.yaml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/.github/workflows/python-app.yaml b/.github/workflows/python-app.yaml index 7bd47a52..30effcdd 100644 --- a/.github/workflows/python-app.yaml +++ b/.github/workflows/python-app.yaml @@ -36,7 +36,6 @@ jobs: wget ftp://ftp.fluxdata.org/.ameriflux_downloads/.test/US-ARc_sample_output.zip unzip US-ARc_sample_input.zip -d ./datadir/test_input/ unzip US-ARc_sample_output.zip -d ./datadir/test_output/ - - name: Run OneFLUX partitioning_nt run: | # copy necessary output data to force partitioning_nt to run @@ -44,13 +43,9 @@ jobs: cp -r ./datadir/test_output/US-ARc_sample_output/07_meteo_proc/ ./datadir/test_input/US-ARc_sample_input/ cp -r ./datadir/test_output/US-ARc_sample_output/08_nee_proc/ ./datadir/test_input/US-ARc_sample_input/ python runoneflux.py partition_nt ./datadir/test_input/ US-ARc US-ARc_sample_input 2005 2006 -l fluxnet_pipeline_US-ARc.log --recint hh - - name: Run pytest run: | pytest oneflux/tools/partition_nt.py - - - # - name: Lint with flake8 # run: | # # stop the build if there are Python syntax errors or undefined names