Fixing miscaleneous PEP8 issues

pycif/__init__.py

 from __future__ import absolute_import
-from .plugins import *
+from .plugins import chemistries, domains, fields, fluxes, measurements, \
+    meteos, minimizers, models, modes, obsoperators, obsparsers, obsvects, \
+    platforms, simulators, statevect, transforms
 
 
 from os.path import dirname, basename, isdir

pycif/plugins/chemistries/__init__.py

@@ -11,4 +11,3 @@ import glob
 modules = glob.glob(dirname(__file__) + "/*")
 
 __all__ = [basename(f) for f in modules if isdir(f) and not f.endswith(".py")]
-

pycif/plugins/chemistries/chimere/read_chemistry.py

@@ -73,5 +73,6 @@ def read_chemicalscheme(chemistry, **kwargs):
     with open(dirchem_ref + "FAMILIES." + chemistry.schemeid, "r") as fsp:
         ln = fsp.readlines()
         chemistry.nfamilies = len(ln)
-
-    chemistry.nprspecies = 4  ##### en dur pour le moment
+    
+    # TODO: generalize number of prescribed species
+    chemistry.nprspecies = 4

pycif/plugins/domains/__init__.py

@@ -11,4 +11,3 @@ import glob
 modules = glob.glob(dirname(__file__) + "/*")
 
 __all__ = [basename(f) for f in modules if isdir(f) and not f.endswith(".py")]
-

pycif/plugins/domains/chimere/create_domain.py

+from pycif.utils.check import info
+
+
 def create_domain(domain, **kwargs):
     """Creates a grid if needed
 

pycif/plugins/domains/lmdz/create_domain.py

+from pycif.utils.check import info
+
+
 def create_domain(domain, **kwargs):
     """Creates a grid if needed
 

pycif/plugins/fields/__init__.py

@@ -11,4 +11,3 @@ import glob
 modules = glob.glob(dirname(__file__) + "/*")
 
 __all__ = [basename(f) for f in modules if isdir(f) and not f.endswith(".py")]
-

pycif/plugins/fluxes/__init__.py

@@ -11,4 +11,3 @@ import glob
 modules = glob.glob(dirname(__file__) + "/*")
 
 __all__ = [basename(f) for f in modules if isdir(f) and not f.endswith(".py")]
-

pycif/plugins/measurements/__init__.py

@@ -6,4 +6,3 @@ import glob
 modules = glob.glob(dirname(__file__) + "/*")
 
 __all__ = [basename(f) for f in modules if isdir(f) and not f.endswith(".py")]
-

pycif/plugins/meteos/__init__.py

@@ -6,4 +6,3 @@ import glob
 modules = glob.glob(dirname(__file__) + "/*")
 
 __all__ = [basename(f) for f in modules if isdir(f) and not f.endswith(".py")]
-

pycif/plugins/meteos/lmdz_massflx/read.py

@@ -21,7 +21,6 @@ def read(
     filetypes=["defstoke", "fluxstoke", "fluxstokev", "phystoke"],
     **kwargs
 ):
-
     """Reads meteorology and links to the working directory
 
     Args:

pycif/plugins/minimizers/__init__.py

@@ -6,4 +6,3 @@ import glob
 modules = glob.glob(dirname(__file__) + "/*")
 
 __all__ = [basename(f) for f in modules if isdir(f) and not f.endswith(".py")]
-

pycif/plugins/minimizers/congrad/minimize.py

@@ -8,7 +8,6 @@ from pycif.utils.check import info
 def minimize(self, finit, gradinit, chi0, **kwargs):
     # x, f, g, auxil, io, niter, nsim, iz, df1, m=5, dxmin=1.e-20,
     #  epsg=1.e-20, impres=1, mode=0, **kwargs
-
     """Entry point for CONGRAD algorithm.
 
     Args:

pycif/plugins/minimizers/m1qn3/minimize.py

@@ -7,7 +7,6 @@ from pycif.utils.check import info
 def minimize(self, finit, gradinit, chi0, **kwargs):
     # x, f, g, auxil, io, niter, nsim, iz, df1, m=5, dxmin=1.e-20,
     #  epsg=1.e-20, impres=1, mode=0, **kwargs
-
     """Entry point for M1QN3 algorithm.
 
     Args:

pycif/plugins/minimizers/m1qn3/opt.py

@@ -78,6 +78,7 @@ def m1qn3(self, f, g, chi, **kwargs):
     eps1 = 1.0
 
     ps = np.dot(g, g)
+    dk = ps
     gnorm = ps
     gnorm = np.sqrt(gnorm)
     if nverbose >= 1:

pycif/plugins/models/__init__.py

@@ -11,4 +11,3 @@ import glob
 modules = glob.glob(dirname(__file__) + "/*")
 
 __all__ = [basename(f) for f in modules if isdir(f) and not f.endswith(".py")]
-

pycif/plugins/models/lmdz/__init__.py

@@ -2,8 +2,8 @@ from __future__ import absolute_import
 import os
 import shutil
 
-from .inputs.fluxes import *
-from .inputs.meteo import *
+from .inputs.fluxes import make_fluxes
+from .inputs.meteo import make_meteo
 from pycif.utils import path
 from pycif.utils.check import info
 from pycif.utils.classes.setup import Setup

pycif/plugins/models/lmdz/inputs/__init__.py

@@ -3,6 +3,7 @@ import os
 import shutil
 
 from .params import make_rundef, make_totinput
+from .meteo import make_meteo
 from pycif.utils import path
 from pycif.utils.check import info
 
@@ -32,25 +33,7 @@ def make_input(
     datei = min(di, df)
 
     if mod_input == "meteo":
-        dir_meteo = data.datastore[("meteo", "")]["dirorig"]
-        # Links meteorological mass fluxes
-        for ftype in ["defstoke", "fluxstoke", "fluxstokev", "phystoke"]:
-            meteo_file = "{}.an{}.m{:02d}.nc".format(
-                ftype, datei.year, datei.month
-            )
-            source = "{}/{}".format(dir_meteo, meteo_file)
-            target = "{}/{}.nc".format(runsubdir, ftype)
-
-            if ftype == "defstoke" and not os.path.isfile(source):
-                meteo_file = "{}.nc".format(ftype)
-                source = "{}/{}".format(dir_meteo, meteo_file)
-
-            path.link(source, target)
-
-        # Links vertical coordinates from previous simulations
-        source = self.file_vcoord
-        target = "{}/vcoord.nc".format(runsubdir)
-        path.link(source, target)
+        make_meteo(self, data, di, df, runsubdir, mode)
 
     elif mod_input == "def":
         # run.def

pycif/plugins/models/lmdz/inputs/chemfields.py

@@ -44,7 +44,7 @@ def make_chemfields(self, data_in, input_type, ddi, ddf, runsubdir, mode):
         path.link(origin, target)
 
         # Skip if that species is not in the control vector
-        if not "spec" in data:
+        if "spec" not in data:
             continue
 
         # If tangent-linear mode, include tl increments
@@ -57,7 +57,7 @@ def make_chemfields(self, data_in, input_type, ddi, ddf, runsubdir, mode):
         prod_file = "{}/mod_{}_{}.bin".format(runsubdir, bin_name, spec)
         with FortranFile(prod_file, "w") as f:
             # Looping over all values and writing to binary
-            prod = prod.values
-            incr = incr.values
+            prod = data["spec"].values
+            incr = data["incr"].values
             for d0, d1 in zip(np.ravel(prod), np.ravel(incr)):
                 f.write_record(np.array([d0, d1], dtype=float))

pycif/plugins/models/lmdz/inputs/meteo.py

 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
+import os
+
+from pycif.utils import path
+
+
+def make_meteo(self, data, ddi, ddf, runsubdir, mode):
+    datei = min(ddi, ddf)
+    
+    dir_meteo = data.datastore[("meteo", "")]["dirorig"]
+    # Links meteorological mass fluxes
+    for ftype in ["defstoke", "fluxstoke", "fluxstokev", "phystoke"]:
+        meteo_file = "{}.an{}.m{:02d}.nc".format(
+            ftype, datei.year, datei.month
+        )
+        source = "{}/{}".format(dir_meteo, meteo_file)
+        target = "{}/{}.nc".format(runsubdir, ftype)
+
+        if ftype == "defstoke" and not os.path.isfile(source):
+            meteo_file = "{}.nc".format(ftype)
+            source = "{}/{}".format(dir_meteo, meteo_file)
+
+        path.link(source, target)
+
+    # Links vertical coordinates from previous simulations
+    source = self.file_vcoord
+    target = "{}/vcoord.nc".format(runsubdir)
+    path.link(source, target)