diff --git a/ci/requirements.txt b/ci/requirements.txt index 196b390..623994f 100644 --- a/ci/requirements.txt +++ b/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 diff --git a/ci/requirements_dev.txt b/ci/requirements_dev.txt index d9c9f01..45ccfd8 100644 --- a/ci/requirements_dev.txt +++ b/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 diff --git a/notebooks/mpl_plot_settings.py b/notebooks/mpl_plot_settings.py index 23dc398..0a462ef 100644 --- a/notebooks/mpl_plot_settings.py +++ b/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 diff --git a/src/EcoFOCIpy/io/adcp_parser.py b/src/EcoFOCIpy/io/adcp_parser.py index 0cea8d5..64c36ec 100644 --- a/src/EcoFOCIpy/io/adcp_parser.py +++ b/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") diff --git a/src/EcoFOCIpy/io/rcm_parser.py b/src/EcoFOCIpy/io/rcm_parser.py index 216e56f..0680da3 100644 --- a/src/EcoFOCIpy/io/rcm_parser.py +++ b/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" diff --git a/src/EcoFOCIpy/io/sbe_parser.py b/src/EcoFOCIpy/io/sbe_parser.py index 67eaf74..8054635 100644 --- a/src/EcoFOCIpy/io/sbe_parser.py +++ b/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(), diff --git a/src/EcoFOCIpy/io/wetlabs_parser.py b/src/EcoFOCIpy/io/wetlabs_parser.py index d7eb38f..e4e3f69 100644 --- a/src/EcoFOCIpy/io/wetlabs_parser.py +++ b/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) diff --git a/src/EcoFOCIpy/io/wpak_parser.py b/src/EcoFOCIpy/io/wpak_parser.py index bbab330..ab47455 100644 --- a/src/EcoFOCIpy/io/wpak_parser.py +++ b/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" ) diff --git a/src/EcoFOCIpy/plots/TimeSeriesStickPlot.py b/src/EcoFOCIpy/plots/TimeSeriesStickPlot.py index 3fd2112..6be30d6 100644 --- a/src/EcoFOCIpy/plots/TimeSeriesStickPlot.py +++ b/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', diff --git a/src/EcoFOCIpy/plots/sbe_ctd_plots.py b/src/EcoFOCIpy/plots/sbe_ctd_plots.py index 724e343..bee0c0a 100644 --- a/src/EcoFOCIpy/plots/sbe_ctd_plots.py +++ b/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',