Merge pull request #45 from zmoon/ci

CI: Python-focused automatic linting/formatting

.flake8

@@ -0,0 +1,3 @@
+[flake8]
+max-line-length = 100
+ignore = E203,E402,E501,W503,E226

.github/workflows/lint.yml

@@ -0,0 +1,18 @@
+name: Lint
+
+on:
+  push:
+    branches: [develop]
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  lint:
+    name: pre-commit
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - uses: pre-commit/[email protected]

.pre-commit-config.yaml

@@ -0,0 +1,35 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.5.0"
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+
+  - repo: https://github.com/asottile/pyupgrade
+    rev: "v3.15.2"
+    hooks:
+      - id: pyupgrade
+        args: [--py37-plus]
+
+  - repo: https://github.com/PyCQA/isort
+    rev: "5.13.2"
+    hooks:
+      - id: isort
+
+  - repo: https://github.com/psf/black
+    rev: "24.3.0"
+    hooks:
+      - id: black
+
+  - repo: https://github.com/PyCQA/flake8
+    rev: "7.0.0"
+    hooks:
+      - id: flake8
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli

README.md

@@ -14,6 +14,12 @@ git clone -b develop --recurse-submodules [email protected]:noaa-oar-arl/NEXUS.git
 ```
 (Replace `noaa-oar-arl` with your fork if desired.)
 
+To install the pre-commit hooks, first [install `pre-commit`](https://pre-commit.com/#install),
+e.g. to your Conda environment.
+Then, run
+```
+pre-commit install --install-hooks
+```
 
 ### Setup
 

cmake/FindNetCDF.cmake

@@ -7,7 +7,7 @@
 # does it submit to any jurisdiction.
 #
 # Try to find NetCDF includes and library.
-# Supports static and shared libaries and allows each component to be found in sepearte prefixes.
+# Supports static and shared libraries and allows each component to be found in separate prefixes.
 #
 # This module defines
 #

config/cmaq/HEMCO_sa_Diagn.rc

@@ -1,7 +1,7 @@
 # This file defines the diagnostics to be written
 # out by the HEMCO standalone model
 #
-# Name      Spec ExtNr Cat Hier Dim Unit   
+# Name      Spec ExtNr Cat Hier Dim Unit
 CO_ant           CO             0    -1  -1   2   kg/m2/s
 SO2_ant          SO2            0    -1  -1   2   kg/m2/s
 NO2_ant          NO2            0    -1  -1   2   kg/m2/s

config/cmaq/HEMCO_sa_Spec.rc

@@ -1,7 +1,7 @@
 # List species below. For each species, the following entries must be given:
 # ID        : species ID
 # NAME      : species name
-# MW        : molecular weight (g/mol) 
+# MW        : molecular weight (g/mol)
 # K0        : Henry constant at 298 K (M/atm, liquid over gas)
 # CR        : Henry temperature dependency (-d ln(KH)/d(1/T)
 # pKA       : acid dissociation constant
@@ -23,7 +23,7 @@
 14 IOLE         56.1  12.0 4.0  0.0 0.0 0.0
 15 OLE          42.1  12.0 2.0  0.0 0.0 0.0
 16 ETH          28.1  12.0 2.0  0.0 0.0 0.0
-17 ETHA         30.1  12.0 2.0  0.0 0.0 0.0 
+17 ETHA         30.1  12.0 2.0  0.0 0.0 0.0
 18 ETOH         46.1  12.0 2.0  0.0 0.0 0.0
 19 MEOH         32.0  12.0 1.0  0.0 0.0 0.0
 20 BENZ         78.1  12.0 6.0  0.0 0.0 0.0

config/cmaq/HEMCO_sa_Time.rc

@@ -1,4 +1,4 @@
-# List here simulation start, end, and emission time step (seconds). 
+# List here simulation start, end, and emission time step (seconds).
 # Dates must have format YYYY-MM-DD HH:MM:SS
 START:   2016-01-05 00:00:00
 END:     2016-01-05 23:00:00

config/cmaq/NEXUS_Config.rc

@@ -6,33 +6,33 @@
 # !MODULE: HEMCO_Config.rc
 #
 # !DESCRIPTION: Contains configuration information for HEMCO. Define the
-#  emissions inventories and corresponding file paths here. Entire 
+#  emissions inventories and corresponding file paths here. Entire
 #  configuration files can be inserted into this configuration file with
-#  an '>>>include' statement, e.g. '>>>include HEMCO\_Config\_test.rc' 
+#  an '>>>include' statement, e.g. '>>>include HEMCO\_Config\_test.rc'
 #  The settings of include-files will be ignored.
 #\\
 #\\
 # !REMARKS:
 #  The following tokens will be replaced:
 #  (1) ROOT    : Filepath to HEMCO root directory
-#  (2) CFDIR   : Filepath to directory of this configuration file. 
+#  (2) CFDIR   : Filepath to directory of this configuration file.
 #  (3) MET     : Met field type (from G-C compilation command)
 #  (4) GRID    : Horizontal grid type (from G-C compilation command)
 #  (5) SIM     : Simulation type (from G-C compilation command)
 #  (6) NEST    : Nested-grid type (CH, EU, NA, SE)
 #  (7) LNOX    : String for OTD/LIS lightning NOx files:
-#                (a) For GEOS-5 this is either "geos5.1.0" or "geos5.2.0".  
+#                (a) For GEOS-5 this is either "geos5.1.0" or "geos5.2.0".
 #                (b) For other met fields, this is the same as MET.
 #  (8) LEVRED  : String w/ the # of levels in the reduced GEOS-Chem grid
 #                as used in some filenames (e.g. "23L", "30L", "47L")
 #  (9) LEVFULL : String w/ the # of levels in the full GEOS-Chem grid
 #                as used in some filenames (e.g. "55L", "72L")
-# 
-# !REVISION HISTORY: 
-#  09 Mar 2021 - P. Campbell - Initial UFS-CMAQ HEMCO Configuration File for 
+#
+# !REVISION HISTORY:
+#  09 Mar 2021 - P. Campbell - Initial UFS-CMAQ HEMCO Configuration File for
 #                              CEDS2019-NEI2016v1-OMI-HTAP2019-EDGAR-HTAP2010
 #  15 Jun 2022 - P. Campbell - Added MEGANv2.1 sa extension calcultaions
-#  04 Oct 2022 - B. Baker    - Remove point sources 
+#  04 Oct 2022 - B. Baker    - Remove point sources
 
 #------------------------------------------------------------------------------
 #BOC
@@ -66,11 +66,11 @@ Cap time shift              : true
 ### BEGIN SECTION EXTENSION SWITCHES
 ###############################################################################
 ###
-### This section lists all emission extensions available to HEMCO and whether 
-### they shall be used or not. Extension 'base' must have extension number 
-### zero, all other extension numbers can be freely chosen. Data fields in 
-### section 'base emissions' will only be read if the corresponding extension 
-### (identified by ExtNr) is enabled. Similarly, fields grouped into data 
+### This section lists all emission extensions available to HEMCO and whether
+### they shall be used or not. Extension 'base' must have extension number
+### zero, all other extension numbers can be freely chosen. Data fields in
+### section 'base emissions' will only be read if the corresponding extension
+### (identified by ExtNr) is enabled. Similarly, fields grouped into data
 ### collections ('(((CollectionName', ')))CollectionName') are only considered
 ### if the corresponding data collection is enabled in this section. Data
 ### listed within a disabled extension are always ignored, even if they are
@@ -81,22 +81,22 @@ Cap time shift              : true
 ### collection name is *not* enabled. This is achieved by leading the
 ### collection name with '.not.', e.g. '(((.not.FINN_daily' ...
 ### '))).not.FINN_daily' for FINN monthly data (only used if daily data is
-### not being used). 
+### not being used).
 ###
 ### The ExtNr provided in this section must match with the ExtNr assigned to
-### the data listed in the base emissions sections. Otherwise, the listed 
+### the data listed in the base emissions sections. Otherwise, the listed
 ### files won't be read!
 ###
 ### NOTES:
 ### --> You can only select one biomass burning option (GFED, QFED, FINN).
 ###
 ### --> BOND_BIOMASS must be set to false if GFED, QFED, or FINN is enabled.
 ###
-### --> The biomass burning POA scale factor is the same as for the biofuel 
-###     and anthro sources. 
+### --> The biomass burning POA scale factor is the same as for the biofuel
+###     and anthro sources.
 ###
 ### --> The NAP scale factor is determined as in the original simulation:
-###     Obtain NAP emissions using scale factor from Hays 2002 ES&T 
+###     Obtain NAP emissions using scale factor from Hays 2002 ES&T
 ###     (0.0253 g NAP/kg DM) and Andreae and Merlet 2001 GBC (92 g CO/kg DM)
 ###############################################################################
 # ExtNr ExtName           on/off  Species
@@ -110,7 +110,7 @@ Cap time shift              : true
     --> C2H6              :       false
     --> EDGAR             :       false
     --> HTAP              :  on   true
-    --> EMEP              :       false 
+    --> EMEP              :       false
     --> GEIA              :       false
     --> LIANG_BROMOCARB   :       false
     --> NEI2005           :       false
@@ -122,7 +122,7 @@ Cap time shift              : true
     --> MIX               :       false
     --> STREETS           :       false
     --> VOLCANO           :       false
-    --> RCP_3PD           :       false 
+    --> RCP_3PD           :       false
     --> RCP_45            :       false
     --> RCP_60            :       false
     --> RCP_85            :       false
@@ -136,25 +136,25 @@ Cap time shift              : true
     --> MODIS_XLAI        :       false
     --> OFFLINE_SOILNOX   :  on   true
 # -----------------------------------------------------------------------------
-100     Custom            : off   - 
+100     Custom            : off   -
 101     SeaFlux           : off   DMS/ACET
 102     ParaNOx           : off   NO/NO2/O3/HNO3
     --> LUT data format   :       nc
     --> LUT source dir    :       $ROOT/PARANOX/v2015-02
 103     LightNOx          : off   NO
     --> OTD-LIS factors   :       true
     --> CDF table         :       $ROOT/LIGHTNOX/v2014-07/light_dist.ott2010.dat
-104     SoilNOx           : off   NO 
+104     SoilNOx           : off   NO
     --> Use fertilizer NOx:       true
-105     DustDead          : off   DST1/DST2/DST3/DST4 
+105     DustDead          : off   DST1/DST2/DST3/DST4
 106     DustGinoux        : off   DST1/DST2/DST3/DST4
 107     SeaSalt           : off   SALA/SALC/Br2
-    --> SALA lower radius :       0.01 
+    --> SALA lower radius :       0.01
     --> SALA upper radius :       0.5
     --> SALC lower radius :       0.5
     --> SALC upper radius :       8.0
-    --> Emit Br2          :       true  
-    --> Br2 scaling       :       1.0 
+    --> Emit Br2          :       true
+    --> Br2 scaling       :       1.0
 108     MEGAN             : on    ISOP/ACET/PRPE/C2H4/ALD2/EOH/MOH/MTPA/MTPO/LIMO/SESQ
     --> Isoprene scaling  :       1.0
     --> CO2 inhibition    :       true
@@ -163,7 +163,7 @@ Cap time shift              : true
     --> Isoprene to SOAS  :       0.015
 110     MEGAN_SOA         : off   MTPA/MTPO/LIMO/SESQ
 111     GFED              : off   NO/CO/ALK4/ACET/MEK/ALD2/PRPE/C3H8/CH2O/C2H6/SO2/NH3/BCPO/BCPI/OCPO/OCPI/POA1/NAP
-    --> GFED3             :       false 
+    --> GFED3             :       false
     --> GFED4             :       true
     --> GFED_daily        :       false
     --> GFED_3hourly      :       false
@@ -181,7 +181,7 @@ Cap time shift              : true
 ### END SECTION EXTENSION SWITCHES ###
 
 ###############################################################################
-### BEGIN SECTION BASE EMISSIONS 
+### BEGIN SECTION BASE EMISSIONS
 ###############################################################################
 
 # ExtNr	Name sourceFile	sourceVar sourceTime C/R/E SrcDim SrcUnit Species ScalIDs Cat Hier
@@ -565,7 +565,7 @@ Cap time shift              : true
 # %%% NOTE: This is an optional inventory. You may select either EDGAR or HTAP
 # for the global base emissions %%%
 # SHP (ships) and AIR_LTO (aircraft landing & take off < 1 km) sectors are included here.
-#============================================================================== 
+#==============================================================================
 (((HTAP
 0 HTAP_PMC_AIR    $ROOT/HTAP/v2015-03/PMC/EDGAR_HTAP_PMC_AIR_LTO.generic.01x01.nc      emi_pmc  2008-2010/1-12/1/0 C xy kg/m2/s PMC   1/27/25  1/2 1
 0 HTAP_PMC_SHP    $ROOT/HTAP/v2015-03/PMC/EDGAR_HTAP_PMC_SHIPS.generic.01x01.nc        emi_pmc  2008-2010/1-12/1/0 C xy kg/m2/s PMC   1/27/25  1/2 1
@@ -1362,7 +1362,7 @@ Cap time shift              : true
 0 NEI2016v1_NPOILGAS_PSO4           $ROOT/NEI2016v1/v2022-07/$MM/NEI2016v1_0.1x0.1_2016$MM$DD_np_oilgas.nc          PSO4          2016/1-12/1-31/$HH C xyz  kg/m2/s  PSO4        1007     1 50
 )))NEI2016v1_AR
 
-#### MEGAN EMISSION 
+#### MEGAN EMISSION
 108  MEGAN_AEF_ISOP               $ROOT/MEGAN/v2020-02/MEGAN2.1_EF.geos.025x03125.nc      AEF_ISOPRENE            1985/1/1/0        C xy kgC/m2/s * 61 1 1
 108  MEGAN_AEF_MBOX               $ROOT/MEGAN/v2020-02/MEGAN2.1_EF.geos.025x03125.nc      AEF_MBO                 1985/1/1/0        C xy kgC/m2/s * 64 1 1
 #108 MEGAN_AEF_APIN               $ROOT/MEGAN/v2020-02/MEGAN2.1_EF.geos.025x03125.nc      AEF_ALPHA_PINENE        1985/1/1/0        C xy kgC/m2/s * 62 1 1
@@ -1664,10 +1664,10 @@ Cap time shift              : true
 ###############################################################################
 ### NON-EMISSIONS DATA (subsection of BASE EMISSIONS SECTION)
 ###
-### Non-emissions data. The following fields are read through HEMCO but do 
-### not contain emissions data. The extension number is set to wildcard 
-### character denoting that these fields will not be considered for emission 
-### calculation. A given entry is only read if the assigned species name is 
+### Non-emissions data. The following fields are read through HEMCO but do
+### not contain emissions data. The extension number is set to wildcard
+### character denoting that these fields will not be considered for emission
+### calculation. A given entry is only read if the assigned species name is
 ### an HEMCO species.
 ###############################################################################
 
@@ -1679,7 +1679,7 @@ Cap time shift              : true
 ### END SECTION BASE EMISSIONS ###
 
 ###############################################################################
-### BEGIN SECTION SCALE FACTORS 
+### BEGIN SECTION SCALE FACTORS
 ###############################################################################
 
 # ScalID Name sourceFile sourceVar sourceTime C/R/E SrcDim SrcUnit Oper
@@ -1697,7 +1697,7 @@ Cap time shift              : true
 27 TOTFUEL_2008_2010 $ROOT/AnnualScalar/v2014-07/AnnualScalar.geos.1x1.nc NOxscalar 2008-2010/1/1/0 C xy 1 -1
 
 #==============================================================================
-# --- diurnal scale factors --- 
+# --- diurnal scale factors ---
 #==============================================================================
 25 EDGAR_TODNOX $ROOT/EDGARv42/v2015-02/NO/EDGAR_hourly_NOxScal.nc NOXscale 2000/1/1/HH C xy unitless 1
 
@@ -1723,7 +1723,7 @@ Cap time shift              : true
 999 NOx_to_NO            0.9                    - - - xy unitless 1
 998 NOx_to_NO2           0.1                    - - - xy unitless 1
 997 VOC_to_ACET_ag       0.0575823632326        - - - xy unitless 1
-996 VOC_to_ACET_ene      0.00957147100992       - - - xy unitless 1          
+996 VOC_to_ACET_ene      0.00957147100992       - - - xy unitless 1
 995 VOC_to_ACET_ind      0.0440082728517        - - - xy unitless 1
 994 VOC_to_ACET_res      0.039774498589         - - - xy unitless 1
 993 VOC_to_ACET_road     0.0                    - - - xy unitless 1
@@ -1966,7 +1966,7 @@ Cap time shift              : true
 ### END SECTION SCALE FACTORS ###
 
 ###############################################################################
-### BEGIN SECTION MASKS 
+### BEGIN SECTION MASKS
 ###############################################################################
 
 # ScalID Name sourceFile sourceVar sourceTime C/R/E SrcDim SrcUnit Oper Lon1/Lat1/Lon2/Lat2

config/cmaq_gfs_megan/HEMCO_sa_Diagn.rc

@@ -1,7 +1,7 @@
 # This file defines the diagnostics to be written
 # out by the HEMCO standalone model
 #
-# Name      Spec ExtNr Cat Hier Dim Unit   
+# Name      Spec ExtNr Cat Hier Dim Unit
 CO_ant           CO             0    -1  -1   2   kg/m2/s
 SO2_ant          SO2            0    -1  -1   2   kg/m2/s
 NO2_ant          NO2            0    -1  -1   2   kg/m2/s

config/cmaq_gfs_megan/HEMCO_sa_Spec.rc

@@ -1,7 +1,7 @@
 # List species below. For each species, the following entries must be given:
 # ID        : species ID
 # NAME      : species name
-# MW        : molecular weight (g/mol) 
+# MW        : molecular weight (g/mol)
 # K0        : Henry constant at 298 K (M/atm, liquid over gas)
 # CR        : Henry temperature dependency (-d ln(KH)/d(1/T)
 # pKA       : acid dissociation constant
@@ -23,7 +23,7 @@
 14 IOLE         56.1  12.0 4.0  0.0 0.0 0.0
 15 OLE          42.1  12.0 2.0  0.0 0.0 0.0
 16 ETH          28.1  12.0 2.0  0.0 0.0 0.0
-17 ETHA         30.1  12.0 2.0  0.0 0.0 0.0 
+17 ETHA         30.1  12.0 2.0  0.0 0.0 0.0
 18 ETOH         46.1  12.0 2.0  0.0 0.0 0.0
 19 MEOH         32.0  12.0 1.0  0.0 0.0 0.0
 20 BENZ         78.1  12.0 6.0  0.0 0.0 0.0

config/cmaq_gfs_megan/HEMCO_sa_Time.rc

@@ -1,4 +1,4 @@
-# List here simulation start, end, and emission time step (seconds). 
+# List here simulation start, end, and emission time step (seconds).
 # Dates must have format YYYY-MM-DD HH:MM:SS
 START:   2016-01-05 00:00:00
 END:     2016-01-05 23:00:00