From 66ea64daee7dd25d6c98447778a9a26d9483d670 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 15 Oct 2024 07:29:46 -0700 Subject: [PATCH 01/10] MNT: (deps-dev): Bump mysql-connector-python from 9.0.0 to 9.1.0 in /ci (#349) Bumps [mysql-connector-python](https://github.com/mysql/mysql-connector-python) from 9.0.0 to 9.1.0. - [Changelog](https://github.com/mysql/mysql-connector-python/blob/trunk/CHANGES.txt) - [Commits](https://github.com/mysql/mysql-connector-python/compare/9.0.0...9.1.0) --- updated-dependencies: - dependency-name: mysql-connector-python dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- ci/requirements_dev.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ci/requirements_dev.txt b/ci/requirements_dev.txt index a3d6fd0..ef377fa 100644 --- a/ci/requirements_dev.txt +++ b/ci/requirements_dev.txt @@ -6,7 +6,7 @@ xlrd>=1.0.0 netcdf4==1.7.1.post2 cftime==1.6.4 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 From bf9e379958e5697be9814ba561fbd9de7659f9f0 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 15 Oct 2024 10:55:20 -0700 Subject: [PATCH 02/10] MNT: (deps): Bump bottleneck from 1.4.0 to 1.4.1 in /ci (#348) Bumps [bottleneck](https://github.com/pydata/bottleneck) from 1.4.0 to 1.4.1. - [Release notes](https://github.com/pydata/bottleneck/releases) - [Changelog](https://github.com/pydata/bottleneck/blob/master/RELEASE.rst) - [Commits](https://github.com/pydata/bottleneck/compare/v1.4.0...v1.4.1) --- updated-dependencies: - dependency-name: bottleneck dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- ci/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ci/requirements.txt b/ci/requirements.txt index 32af99e..c4b9180 100644 --- a/ci/requirements.txt +++ b/ci/requirements.txt @@ -8,5 +8,5 @@ cftime==1.6.4 erddapy==2.2.3 ctd==1.4.6 #python-ctd seawater==3.3.5 -bottleneck==1.4.0 +bottleneck==1.4.1 #geomag cmweis github version... part of package From 1ba1eac25c9e351be7ddc8ef14c5f9dab8bdfdf0 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 15 Oct 2024 10:55:39 -0700 Subject: [PATCH 03/10] MNT: (deps): Bump numpy from 2.1.1 to 2.1.2 in /ci (#347) Bumps [numpy](https://github.com/numpy/numpy) from 2.1.1 to 2.1.2. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](https://github.com/numpy/numpy/compare/v2.1.1...v2.1.2) --- updated-dependencies: - dependency-name: numpy dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- ci/requirements.txt | 2 +- ci/requirements_dev.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/ci/requirements.txt b/ci/requirements.txt index c4b9180..ed5d874 100644 --- a/ci/requirements.txt +++ b/ci/requirements.txt @@ -1,6 +1,6 @@ #python>=3.8 matplotlib==3.9.2 -numpy==2.1.1 +numpy==2.1.2 pandas==2.2.3 xlrd>=1.0.0 netcdf4==1.7.1.post2 diff --git a/ci/requirements_dev.txt b/ci/requirements_dev.txt index ef377fa..a61804c 100644 --- a/ci/requirements_dev.txt +++ b/ci/requirements_dev.txt @@ -1,6 +1,6 @@ #python>=3.8 matplotlib==3.9.2 -numpy==2.1.1 +numpy==2.1.2 pandas==2.2.3 xlrd>=1.0.0 netcdf4==1.7.1.post2 From 808d1b0d4ebf96e7f93ef836cb8fe84732a929e6 Mon Sep 17 00:00:00 2001 From: shaunwbell Date: Tue, 15 Oct 2024 10:57:49 -0700 Subject: [PATCH 04/10] seaborn ticks (#350) --- notebooks/mpl_plot_settings.py | 2 +- src/EcoFOCIpy/plots/TimeSeriesStickPlot.py | 2 +- src/EcoFOCIpy/plots/sbe_ctd_plots.py | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) 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/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', From 23ccfd9ef2ea3c5b894ddbdfbbf305f3d50ffa2e Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 18 Oct 2024 08:46:19 -0700 Subject: [PATCH 05/10] MNT: (deps): Bump bottleneck from 1.4.1 to 1.4.2 in /ci (#351) Bumps [bottleneck](https://github.com/pydata/bottleneck) from 1.4.1 to 1.4.2. - [Release notes](https://github.com/pydata/bottleneck/releases) - [Changelog](https://github.com/pydata/bottleneck/blob/master/RELEASE.rst) - [Commits](https://github.com/pydata/bottleneck/compare/v1.4.1...v1.4.2) --- updated-dependencies: - dependency-name: bottleneck dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- ci/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ci/requirements.txt b/ci/requirements.txt index ed5d874..299b91f 100644 --- a/ci/requirements.txt +++ b/ci/requirements.txt @@ -8,5 +8,5 @@ cftime==1.6.4 erddapy==2.2.3 ctd==1.4.6 #python-ctd seawater==3.3.5 -bottleneck==1.4.1 +bottleneck==1.4.2 #geomag cmweis github version... part of package From 5ba323074adb0e74b521f63d1c869e16b6a4b9a3 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 24 Oct 2024 07:41:14 -0700 Subject: [PATCH 06/10] MNT: (deps): Bump netcdf4 from 1.7.1.post2 to 1.7.2 in /ci (#353) Bumps [netcdf4](https://github.com/Unidata/netcdf4-python) from 1.7.1.post2 to 1.7.2. - [Release notes](https://github.com/Unidata/netcdf4-python/releases) - [Changelog](https://github.com/Unidata/netcdf4-python/blob/master/Changelog) - [Commits](https://github.com/Unidata/netcdf4-python/commits) --- updated-dependencies: - dependency-name: netcdf4 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- ci/requirements.txt | 2 +- ci/requirements_dev.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/ci/requirements.txt b/ci/requirements.txt index 299b91f..a0fddf3 100644 --- a/ci/requirements.txt +++ b/ci/requirements.txt @@ -3,7 +3,7 @@ matplotlib==3.9.2 numpy==2.1.2 pandas==2.2.3 xlrd>=1.0.0 -netcdf4==1.7.1.post2 +netcdf4==1.7.2 cftime==1.6.4 erddapy==2.2.3 ctd==1.4.6 #python-ctd diff --git a/ci/requirements_dev.txt b/ci/requirements_dev.txt index a61804c..cef8bd9 100644 --- a/ci/requirements_dev.txt +++ b/ci/requirements_dev.txt @@ -3,7 +3,7 @@ matplotlib==3.9.2 numpy==2.1.2 pandas==2.2.3 xlrd>=1.0.0 -netcdf4==1.7.1.post2 +netcdf4==1.7.2 cftime==1.6.4 erddapy==2.2.3 mysql-connector-python==9.1.0 From 50831033e7f3cf41d0a4b69ce8cf9be625144e71 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 24 Oct 2024 14:42:17 +0000 Subject: [PATCH 07/10] MNT: (deps): Bump cftime from 1.6.4 to 1.6.4.post1 in /ci Bumps [cftime](https://github.com/Unidata/cftime) from 1.6.4 to 1.6.4.post1. - [Release notes](https://github.com/Unidata/cftime/releases) - [Changelog](https://github.com/Unidata/cftime/blob/master/Changelog) - [Commits](https://github.com/Unidata/cftime/commits) --- updated-dependencies: - dependency-name: cftime dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- ci/requirements.txt | 2 +- ci/requirements_dev.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/ci/requirements.txt b/ci/requirements.txt index a0fddf3..d64f565 100644 --- a/ci/requirements.txt +++ b/ci/requirements.txt @@ -4,7 +4,7 @@ numpy==2.1.2 pandas==2.2.3 xlrd>=1.0.0 netcdf4==1.7.2 -cftime==1.6.4 +cftime==1.6.4.post1 erddapy==2.2.3 ctd==1.4.6 #python-ctd seawater==3.3.5 diff --git a/ci/requirements_dev.txt b/ci/requirements_dev.txt index cef8bd9..851b4f6 100644 --- a/ci/requirements_dev.txt +++ b/ci/requirements_dev.txt @@ -4,7 +4,7 @@ numpy==2.1.2 pandas==2.2.3 xlrd>=1.0.0 netcdf4==1.7.2 -cftime==1.6.4 +cftime==1.6.4.post1 erddapy==2.2.3 mysql-connector-python==9.1.0 ctd==1.4.6 #python-ctd From 897bff2a5da838675fb852db896400f529f0a6f4 Mon Sep 17 00:00:00 2001 From: shaunwbell Date: Wed, 30 Oct 2024 07:17:17 -0700 Subject: [PATCH 08/10] Update adcp_parser.py (#354) --- src/EcoFOCIpy/io/adcp_parser.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) 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") From 311aca197d7d39e9a76362d8147f91453c59c6d6 Mon Sep 17 00:00:00 2001 From: shaunwbell Date: Thu, 31 Oct 2024 08:03:01 -0700 Subject: [PATCH 09/10] python 3.12 string updates (#355) --- src/EcoFOCIpy/io/rcm_parser.py | 2 +- src/EcoFOCIpy/io/sbe_parser.py | 6 +++--- src/EcoFOCIpy/io/wetlabs_parser.py | 2 +- src/EcoFOCIpy/io/wpak_parser.py | 2 +- 4 files changed, 6 insertions(+), 6 deletions(-) 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" ) From 199b1f0328b68327d4f5bc244466e315c79cf306 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 4 Nov 2024 08:06:09 -0800 Subject: [PATCH 10/10] MNT: (deps): Bump numpy from 2.1.2 to 2.1.3 in /ci (#356) Bumps [numpy](https://github.com/numpy/numpy) from 2.1.2 to 2.1.3. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](https://github.com/numpy/numpy/compare/v2.1.2...v2.1.3) --- updated-dependencies: - dependency-name: numpy dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- ci/requirements.txt | 2 +- ci/requirements_dev.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/ci/requirements.txt b/ci/requirements.txt index d64f565..492f7c2 100644 --- a/ci/requirements.txt +++ b/ci/requirements.txt @@ -1,6 +1,6 @@ #python>=3.8 matplotlib==3.9.2 -numpy==2.1.2 +numpy==2.1.3 pandas==2.2.3 xlrd>=1.0.0 netcdf4==1.7.2 diff --git a/ci/requirements_dev.txt b/ci/requirements_dev.txt index 851b4f6..26fef06 100644 --- a/ci/requirements_dev.txt +++ b/ci/requirements_dev.txt @@ -1,6 +1,6 @@ #python>=3.8 matplotlib==3.9.2 -numpy==2.1.2 +numpy==2.1.3 pandas==2.2.3 xlrd>=1.0.0 netcdf4==1.7.2