Merge remote-tracking branch 'origin/main' into feature/suna

keep the branch updated

ci/requirements.txt

@@ -1,14 +1,14 @@
 #python>=3.8
 matplotlib==3.9.2
-numpy==2.1.1
+numpy==2.1.3
 pandas==2.2.3
 xlrd>=1.0.0
-netcdf4==1.7.1.post2
-cftime==1.6.4
+netcdf4==1.7.2
+cftime==1.6.4.post1
 erddapy==2.2.3
 ctd==1.4.6 #python-ctd
 seawater==3.3.5
-bottleneck==1.4.0
+bottleneck==1.4.2
 #geomag cmweis github version... part of package
 pyyaml
 requests

ci/requirements_dev.txt

@@ -1,12 +1,12 @@
 #python>=3.8
 matplotlib==3.9.2
-numpy==2.1.1
+numpy==2.1.3
 pandas==2.2.3
 xlrd>=1.0.0
-netcdf4==1.7.1.post2
-cftime==1.6.4
+netcdf4==1.7.2
+cftime==1.6.4.post1
 erddapy==2.2.3
-mysql-connector-python==9.0.0
+mysql-connector-python==9.1.0
 ctd==1.4.6 #python-ctd
 seawater==3.3.5
 #geomag cmweis github version... part of package

notebooks/mpl_plot_settings.py

@@ -7,7 +7,7 @@
 labelsize = 10
 #plotstyle = 'seaborn'
 max_xticks = 10
-plt.style.use('seaborn-ticks')
+plt.style.use('seaborn-v0_8-ticks')
 mpl.rcParams['svg.fonttype'] = 'none'
 mpl.rcParams['ps.fonttype'] = 42 #truetype/type2 fonts instead of type3
 mpl.rcParams['pdf.fonttype'] = 42 #truetype/type2 fonts instead of type3

src/EcoFOCIpy/io/adcp_parser.py

@@ -37,7 +37,7 @@ def load_pg_file(self, pgfile_path=None, datetime_index=True):
         if self.depdir:
             pgfile_path = self.depdir + '.PG'
 
-        self.pg_df = pd.read_csv(pgfile_path,delimiter='\s+',header=None,names=['date','time','bin','pg3beam-good','pgtransf-good','pg1beam-bad','pg4beam-good'])
+        self.pg_df = pd.read_csv(pgfile_path,delimiter=r'\s+',header=None,names=['date','time','bin','pg3beam-good','pgtransf-good','pg1beam-bad','pg4beam-good'])
         self.pg_df["date_time"] = pd.to_datetime(self.pg_df.date+' '+self.pg_df.time,format="%y/%m/%d %H:%M:%S")
 
         if datetime_index:
@@ -49,7 +49,7 @@ def load_ein_file(self, einfile_path=None, datetime_index=True):
         if self.depdir:
             einfile_path = self.depdir + '.EIN'
 
-        self.ein_df = pd.read_csv(einfile_path,delimiter='\s+',header=None,names=['date','time','bin','agc1','agc2','agc3','agc4'])
+        self.ein_df = pd.read_csv(einfile_path,delimiter=r'\s+',header=None,names=['date','time','bin','agc1','agc2','agc3','agc4'])
         self.ein_df["date_time"] = pd.to_datetime(self.ein_df.date+' '+self.ein_df.time,format="%y/%m/%d %H:%M:%S")
 
         if datetime_index:
@@ -61,7 +61,7 @@ def load_vel_file(self, velfile_path=None, datetime_index=True):
         if self.depdir:
             velfile_path = self.depdir + '.VEL'
 
-        self.vel_df = pd.read_csv(velfile_path,delimiter='\s+',header=None,
+        self.vel_df = pd.read_csv(velfile_path,delimiter=r'\s+',header=None,
                                     names=['date','time','bin','u_curr_comp','v_curr_comp','w_curr_comp','w_curr_comp_err'])
         self.vel_df["date_time"] = pd.to_datetime(self.vel_df.date+' '+self.vel_df.time,format="%y/%m/%d %H:%M:%S")
 
@@ -74,7 +74,7 @@ def load_scal_file(self, scalfile_path=None, datetime_index=True):
         if self.depdir:
             scalfile_path = self.depdir + '.SCA'
 
-        self.scal_df = pd.read_csv(scalfile_path,delimiter='\s+',header=None,
+        self.scal_df = pd.read_csv(scalfile_path,delimiter=r'\s+',header=None,
                                     names=['date','time','unknown','temperature','heading','pitch','roll','heading_stdev','pitch_stdev','roll_stdev'])
         self.scal_df["date_time"] = pd.to_datetime(self.scal_df.date+' '+self.scal_df.time,format="%y/%m/%d %H:%M:%S")
 

src/EcoFOCIpy/io/rcm_parser.py

@@ -62,7 +62,7 @@ def parse(self, filename=None, number_of_channels=8, time_format=0, datetime_ind
         else:
             headernames=['sample','date','time','ident','speed_engr','dir_engr','temp_engr','cond_engr','press_engr']
 
-        rawdata_df = pd.read_csv(filename, names=headernames, delimiter="\s+",)
+        rawdata_df = pd.read_csv(filename, names=headernames, delimiter=r'\s+',)
         if time_format == 0:
             rawdata_df["date_time"] = pd.to_datetime(
                 rawdata_df['date'] + " " + rawdata_df['time'], format="%m/%d/%Y %H:%M:%S"

src/EcoFOCIpy/io/sbe_parser.py

@@ -76,7 +76,7 @@ def parse(filename=None, return_header=True, datetime_index=True):
 
 
         rawdata_df = pd.read_csv(filename, 
-                        delimiter="\s+", 
+                        delimiter=r'\s+', 
                         parse_dates=True, 
                         header=None,
                         names=var_names.values(), 
@@ -131,7 +131,7 @@ def parse(filename=None, datetime_index=True):
         assert filename.split('.')[-1] == 'tid' , 'Must provide a tid file - use sbe software to convert'
 
         rawdata_df = pd.read_csv(filename, 
-                                 delimiter="\s+", 
+                                 delimiter=r'\s+', 
                                  skiprows=1, 
                                  names=["date", "time", "pressure", "temperature"])
 
@@ -289,7 +289,7 @@ def parse(filename=None, return_header=True, datetime_index=True):
 
 
         rawdata_df = pd.read_csv(filename, 
-                        delimiter="\s+", 
+                        delimiter=r'\s+', 
                         parse_dates=True, 
                         header=None,
                         names=var_names.values(), 

src/EcoFOCIpy/io/wetlabs_parser.py

@@ -52,7 +52,7 @@ def parse(self, filename=None, return_header=True, datetime_index=True):
 
 
         rawdata_df = pd.read_csv(filename, 
-                        delimiter="\s+", 
+                        delimiter=r'\s+', 
                         parse_dates=True, 
                         header=None, 
                         skiprows=headercount)       

src/EcoFOCIpy/io/wpak_parser.py

@@ -33,7 +33,7 @@ def parse(filename=None, argos_file=False, datetime_index=True):
         """
         assert filename != None , 'Must provide a datafile'
 
-        rawdata_df = pd.read_csv(filename, header=0, delimiter="\s+")
+        rawdata_df = pd.read_csv(filename, header=0, delimiter=r'\s+')
         rawdata_df["date_time"] = pd.to_datetime(
             rawdata_df["DATE"] + " " + rawdata_df["TIME"], format="%y/%m/%d %H:%M:%S"
         )

src/EcoFOCIpy/plots/TimeSeriesStickPlot.py

@@ -35,7 +35,7 @@ def __init__(self, fontsize=10, labelsize=10, plotstyle='k-.', stylesheet='bmh')
           The fontsize to use for labels
         stylesheet : str
           Choose a mpl stylesheet [u'seaborn-darkgrid', 
-          u'seaborn-notebook', u'classic', u'seaborn-ticks', 
+          u'seaborn-notebook', u'classic', u'seaborn-v0_8-ticks', 
           u'grayscale', u'bmh', u'seaborn-talk', u'dark_background', 
           u'ggplot', u'fivethirtyeight', u'seaborn-colorblind', 
           u'seaborn-deep', u'seaborn-whitegrid', u'seaborn-bright', 

src/EcoFOCIpy/plots/sbe_ctd_plots.py

@@ -16,7 +16,7 @@
 class CTDProfilePlot(object):
 
 
-    def __init__(self, fontsize=10, labelsize=10, plotstyle='k-.', stylesheet='seaborn-ticks'):
+    def __init__(self, fontsize=10, labelsize=10, plotstyle='k-.', stylesheet='seaborn-v0_8-ticks'):
         """Initialize the timeseries with items that do not change.
 
         This sets up the axes and station locations. The `fontsize` and `spacing`
@@ -31,7 +31,7 @@ def __init__(self, fontsize=10, labelsize=10, plotstyle='k-.', stylesheet='seabo
           The fontsize to use for labels
         stylesheet : str
           Choose a mpl stylesheet [u'seaborn-darkgrid', 
-          u'seaborn-notebook', u'classic', u'seaborn-ticks', 
+          u'seaborn-notebook', u'classic', u'seaborn-v0_8-ticks', 
           u'grayscale', u'bmh', u'seaborn-talk', u'dark_background', 
           u'ggplot', u'fivethirtyeight', u'seaborn-colorblind', 
           u'seaborn-deep', u'seaborn-whitegrid', u'seaborn-bright',