made all imports relative; package now works with pip install

I finally have a reason to move away from the iPython environment, and so now all imports should be done properly

.gitignore

@@ -9,7 +9,7 @@
 *.json
 *.bat
 *.log
-
+*.egg-info
 
 /docs/build/*
 .VSCodeCounter/*

inputs/icon_regional_run.py

@@ -1,6 +1,6 @@
 import numpy as np
-from src import var, utils
-from inputs import local_paths
+from ..src import var, utils
+from ..inputs import local_paths
 
 params = var.params()
 
@@ -23,6 +23,8 @@
 
 params.tri_set = [13, 104, 105, 106]
 
+params.merit_cg = 20
+
 # Setup the Fourier parameters and object.
 params.nhi = 24
 params.nhj = 48
@@ -34,7 +36,7 @@
 params.rect = True
 
 params.debug = False
-params.dfft_first_guess = True
+params.dfft_first_guess = False
 params.refine = False
 params.verbose = False
 

inputs/local_paths_example.py

@@ -1,4 +1,4 @@
-from src import var
+from ..src import var
 
 paths = var.obj()
 

pyproject.toml

@@ -1,3 +1,30 @@
+[project]
+name = "pyCSAM"
+version = "0.95.1"
+
+dependencies = [
+    "Cartopy==0.21.1",
+    "h5py==3.9.0",
+    "ipython==8.12.3",
+    "matplotlib==3.7.2",
+    "netCDF4==1.6.5",
+    "noise==1.2.2",
+    "numba==0.57.1",
+    "numpy==1.24.3",
+    "pandas==2.0.3",
+    "scikit_learn==1.3.0",
+    "scipy==1.12.0",
+]
+
+# Packaging
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+package-dir = {"pycsam" = ""}
+
+
 [tool.towncrier]
 directory = "changelog.d"
 filename = "CHANGELOG.rst"

src/io.py

@@ -8,7 +8,7 @@
 import os
 from datetime import datetime
 
-from src import utils
+from ..src import utils
 
 
 class ncdata(object):
@@ -570,40 +570,52 @@ def __init__(self, params):
 
         rootgrp = nc.Dataset(self.path + self.fn, "w", format="NETCDF4")
 
+        for key, value in vars(params).items():
+
+            # if params attribute is None but check passed, then the attribute is not necessary for the run; skip it
+            if value is None:
+                continue
+            # NetCDF does not accept Boolean types; convert to int
+            if type(value) is bool:
+                value = int(value)
+            # Else, write attribute
+            setattr(rootgrp, key, value)
+
         _ = rootgrp.createDimension("nspec", params.n_modes)
 
         self.n_modes = params.n_modes
         rootgrp.close()
 
-    def output(self, id, clat, clon, analysis):
+    def output(self, id, clat, clon, is_land, analysis=None):
 
         rootgrp = nc.Dataset(self.path + self.fn, "a", format="NETCDF4")
 
         grp = rootgrp.createGroup(str(id))
 
         is_land_var = grp.createVariable("is_land","i4")
-        is_land_var[:] = 1
+        is_land_var[:] = is_land
 
         clat_var = grp.createVariable("clat","f8")
         clat_var[:] = clat
         clon_var = grp.createVariable("clon","f8")
         clon_var[:] = clon
 
-        dk_var = grp.createVariable("dk","f8")
-        dk_var[:] = analysis.dk
-        dl_var = grp.createVariable("dl","f8")
-        dl_var[:] = analysis.dl
+        if analysis is not None:
+            dk_var = grp.createVariable("dk","f8")
+            dk_var[:] = analysis.dk
+            dl_var = grp.createVariable("dl","f8")
+            dl_var[:] = analysis.dl
 
-        pick_idx = np.where(analysis.ampls > 0)
+            pick_idx = np.where(analysis.ampls > 0)
 
-        H_spec_var = grp.createVariable("H_spec","f8", ("nspec",))
-        H_spec_var[:] = self.__pad_zeros(analysis.ampls[pick_idx], self.n_modes)
+            H_spec_var = grp.createVariable("H_spec","f8", ("nspec",))
+            H_spec_var[:] = self.__pad_zeros(analysis.ampls[pick_idx], self.n_modes)
 
-        kks_var = grp.createVariable("kks","f8", ("nspec",))
-        kks_var[:] = self.__pad_zeros(analysis.kks[pick_idx], self.n_modes)
+            kks_var = grp.createVariable("kks","f8", ("nspec",))
+            kks_var[:] = self.__pad_zeros(analysis.kks[pick_idx], self.n_modes)
 
-        lls_var = grp.createVariable("lls","f8", ("nspec",))
-        lls_var[:] = self.__pad_zeros(analysis.lls[pick_idx], self.n_modes)
+            lls_var = grp.createVariable("lls","f8", ("nspec",))
+            lls_var[:] = self.__pad_zeros(analysis.lls[pick_idx], self.n_modes)
 
         rootgrp.close()
 

src/utils.py

@@ -818,4 +818,16 @@ def transfer_attributes(params, cls, prefix=""):
         if not hasattr(params, key):
             setattr(params, key, value)
         elif getattr(params, key) == None:
-            setattr(params, key, value)
+            setattr(params, key, value)
+
+
+def is_land(cell, simplex_lat, simplex_lon, topo, height_tol=0.5, percent_tol=0.95):
+
+    get_lat_lon_segments(
+    simplex_lat, simplex_lon, cell, topo, load_topo=True, filtered=False
+    ) 
+
+    if not (((cell.topo <= height_tol).sum() / cell.topo.size) > percent_tol):
+        return False
+    else:
+        return True

src/var.py

@@ -3,7 +3,7 @@
 """
 
 import numpy as np
-from src import utils, io
+from ..src import utils, io
 
 
 class grid(object):

wrappers/interface.py

@@ -3,8 +3,8 @@
 """
 
 
-from src import fourier, lin_reg, physics, reconstruction
-from src import utils, var
+from ..src import fourier, lin_reg, physics, reconstruction
+from ..src import utils, var
 from copy import deepcopy
 import numpy as np