Merge pull request #101 from rubisco-sfa/deps

FIX: updates to deps and some cleanup

azure-pipelines.yml

@@ -14,15 +14,20 @@ steps:
       versionSpec: "$(python.version)"
     displayName: "Use Python $(python.version)"
 
+  - bash: echo "##vso[task.prependpath]$CONDA/bin"
+    displayName: Add conda to PATH
+
+  - script: conda env create --quiet --file ilamb.yml
+    displayName: Create conda environment
+
   - script: |
-      sudo apt-get -y install libgeos-dev proj-bin libproj-dev libmpich-dev libhdf5-dev
-      python -m pip install --upgrade pip
-      python -m pip install shapely==1.8.5 requests
+      source activate ilamb
       python -m pip install ./
       python -c "import ILAMB; print('ILAMB v%s successfully installed' % (ILAMB.__version__))"
     displayName: "Install ILAMB"
 
   - script: |
+      source activate ilamb
       cd test
       export RDMAV_FORK_SAFE=1
       export ILAMB_ROOT=./

bin/ilamb-run

@@ -8,6 +8,7 @@ mpi4py.rc.threads = False
 import logging
 
 import yaml
+
 from ILAMB.ModelResult import ModelResult
 
 try:
@@ -33,12 +34,13 @@ import matplotlib.colors as clr
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
+from mpi4py import MPI
+from netCDF4 import Dataset
+
 from ILAMB import ilamblib as il
 from ILAMB.Post import RegisterCustomColormaps
 from ILAMB.Regions import Regions
 from ILAMB.Scoreboard import Scoreboard
-from mpi4py import MPI
-from netCDF4 import Dataset
 
 if "wetdry" not in plt.colormaps():
     RegisterCustomColormaps()
@@ -956,8 +958,7 @@ if args.global_region:
 # Setup study
 T0 = time.time()
 if rank == 0:
-    if not os.path.isdir(args.build_dir[0]):
-        os.makedirs(args.build_dir[0])
+    os.makedirs(args.build_dir[0], exist_ok=True)
 if args.model_setup is None:
     M = InitializeModels(
         args.model_root[0],

ilamb.yml

@@ -6,16 +6,18 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python=3
+  - python>=3.9
   - numpy
   - pandas
   - matplotlib
   - cartopy
   - netCDF4
+  - cf-units
   - sympy
-  - scipy
   - mpi4py
-  - cf_units
-  - cython
-  - psutil
+  - scipy
+  - cftime
+  - tqdm
+  - pyarrow
+  - pyyaml
   - requests

setup.py

@@ -109,19 +109,20 @@ def write_version_py(filename=os.path.join("src/ILAMB", "generated_version.py"))
     scripts=["bin/ilamb-run", "bin/ilamb-fetch", "bin/ilamb-mean", "bin/ilamb-setup"],
     zip_safe=False,
     install_requires=[
-        "numpy<2",
-        "pandas>=1.0.0",
-        "matplotlib>=2.2",
-        "cartopy>=0.17.0",
-        "netCDF4>=1.1.4",
-        "cf_units>=2.0.0",
-        "sympy>=0.7.6",
-        "mpi4py>=1.3.1",
-        "scipy>=0.9.0",
+        "numpy",
+        "pandas",
+        "matplotlib",
+        "cartopy",
+        "netCDF4",
+        "cf-units",
+        "sympy",
+        "mpi4py",
+        "scipy",
         "cftime",
         "tqdm",
         "pyarrow",
         "pyyaml",
+        "requests",
     ],
     extras_require={
         "watershed": ["contextily", "geopandas", "dataretrieval", "pynhd"],

test/score_diff.py

@@ -1,20 +1,16 @@
-import numpy as np
 import sys
+
+import numpy as np
+import pandas as pd
+
 if len(sys.argv) != 3:
     print("usage: python score_diff.py scores1.csv scores2.csv")
     sys.exit(1)
-gold = np.recfromcsv(sys.argv[1],encoding=None)
-test = np.recfromcsv(sys.argv[2],encoding=None)
-assert gold.dtype == test.dtype
-ok   = True
-for model in gold.dtype.names[1:]:
-    if not np.allclose(test[model],gold[model]):
-        ok   = False
-        diff = np.abs(test[model]-gold[model])/gold[model]
-        for i in range(diff.size):
-            if diff[i] > 1e-12:
-                print("%s | %s | %.6f%% " % (gold['variables'][i],model,diff[i]*100.))
-if not ok:
+gold = pd.read_csv(sys.argv[1]).set_index("Variables")
+test = pd.read_csv(sys.argv[2]).set_index("Variables")
+diff = np.abs(gold - test) / gold
+if not (diff < 1e12).all()["LandTest"]:
     print("Test failed")
+    print(diff[diff > 1e-12].dropna())
     sys.exit(1)
 print("Test passed")