From ff3f6e02a77007793a161bd1e7ff1e863e6e6e51 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 10 Oct 2022 20:37:58 +0000
Subject: [PATCH 1/7] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/psf/black: 22.8.0 → 22.10.0](https://github.com/psf/black/compare/22.8.0...22.10.0)
- [github.com/asottile/pyupgrade: v2.38.0 → v3.0.0](https://github.com/asottile/pyupgrade/compare/v2.38.0...v3.0.0)
- [github.com/asottile/add-trailing-comma: v2.2.3 → v2.3.0](https://github.com/asottile/add-trailing-comma/compare/v2.2.3...v2.3.0)
---
 .pre-commit-config.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 7c5afb6..5710153 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -35,7 +35,7 @@ repos:
       args: ["--profile", "black", "--filter-files"]
 
 - repo: https://github.com/psf/black
-  rev: 22.8.0
+  rev: 22.10.0
   hooks:
   - id: black
     language_version: python3
@@ -49,13 +49,13 @@ repos:
         - --ignore-words-list=pres,nd,te,afe,ue,wil,tey,te,ot,fo
 
 - repo: https://github.com/asottile/pyupgrade
-  rev: v2.38.0
+  rev: v3.0.0
   hooks:
     - id: pyupgrade
       args:
         - --py36-plus
 
 - repo: https://github.com/asottile/add-trailing-comma
-  rev: v2.2.3
+  rev: v2.3.0
   hooks:
     - id: add-trailing-comma

From 1deb7b055a3514cc4e266218dab307b0578200d4 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 17 Oct 2022 20:12:55 +0000
Subject: [PATCH 2/7] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/codespell-project/codespell: v2.2.1 → v2.2.2](https://github.com/codespell-project/codespell/compare/v2.2.1...v2.2.2)
- [github.com/asottile/pyupgrade: v3.0.0 → v3.1.0](https://github.com/asottile/pyupgrade/compare/v3.0.0...v3.1.0)
---
 .pre-commit-config.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 5710153..2275d10 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -42,14 +42,14 @@ repos:
 
 
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.2.1
+  rev: v2.2.2
   hooks:
     - id: codespell
       args:
         - --ignore-words-list=pres,nd,te,afe,ue,wil,tey,te,ot,fo
 
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.0.0
+  rev: v3.1.0
   hooks:
     - id: pyupgrade
       args:

From e7abfe77cd72828aa10d7851bb4a583a36ab8b9a Mon Sep 17 00:00:00 2001
From: Filipe Fernandes <ocefpaf@gmail.com>
Date: Mon, 24 Oct 2022 15:38:12 -0300
Subject: [PATCH 3/7] run doctests

---
 .github/workflows/tests.yml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index bd5b0c5..9912662 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -34,3 +34,9 @@ jobs:
       run: |
         micromamba activate TEST
         python -m pytest -rxs tests
+
+    - name: Doctests
+      shell: bash -l {0}
+      run: |
+        micromamba activate TEST
+        python -m pytest -s -rxs --doctest-modules -vv ctd

From bdd641cb8be7a3395a850a6113d915b251cb35b2 Mon Sep 17 00:00:00 2001
From: Filipe Fernandes <ocefpaf@gmail.com>
Date: Mon, 24 Oct 2022 15:38:22 -0300
Subject: [PATCH 4/7] remove executable bits

---
 tests/data/castaway_data.csv | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 mode change 100755 => 100644 tests/data/castaway_data.csv

diff --git a/tests/data/castaway_data.csv b/tests/data/castaway_data.csv
old mode 100755
new mode 100644

From ad1cce7178e5195798ed3adc345752655e0a31c9 Mon Sep 17 00:00:00 2001
From: Filipe Fernandes <ocefpaf@gmail.com>
Date: Mon, 24 Oct 2022 15:39:39 -0300
Subject: [PATCH 5/7] fix castaway import

---
 ctd/__init__.py | 11 ++++++++++-
 ctd/read.py     |  8 ++++----
 2 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/ctd/__init__.py b/ctd/__init__.py
index 489b9df..88076fc 100644
--- a/ctd/__init__.py
+++ b/ctd/__init__.py
@@ -15,7 +15,15 @@
     smooth,
     split,
 )
-from .read import from_bl, from_btl, from_cnv, from_edf, from_fsi, rosette_summary
+from .read import (
+    from_bl,
+    from_btl,
+    from_castaway_csv,
+    from_cnv,
+    from_edf,
+    from_fsi,
+    rosette_summary,
+)
 
 try:
     from ._version import __version__
@@ -28,6 +36,7 @@
     "despike",
     "from_bl",
     "from_btl",
+    "from_castaway_csv",
     "from_cnv",
     "from_edf",
     "from_fsi",
diff --git a/ctd/read.py b/ctd/read.py
index 773cebb..c0544f5 100644
--- a/ctd/read.py
+++ b/ctd/read.py
@@ -522,10 +522,10 @@ def from_castaway_csv(fname):
     --------
     >>> import ctd
     >>> cast = ctd.from_castaway_csv('tests/data/castaway_data.csv')
-    >>> downcast, upcast = cast.split() # Upcast often prefiltered
-    >>> fig, ax = plt.subplots()
-    >>> ax = downcast['temperature'].plot_cast()
-    >>> fig.show()
+    >>> cast.columns
+    Index(['depth', 'temperature', 'conductivity', 'specific_conductance',
+           'salinity', 'sound_velocity', 'density'],
+          dtype='object')
 
     """
     with open(fname) as file:

From 6c0b896e8a8a4983cb8cb1efc6bbd010c1d151c8 Mon Sep 17 00:00:00 2001
From: Filipe Fernandes <ocefpaf@gmail.com>
Date: Mon, 24 Oct 2022 16:05:30 -0300
Subject: [PATCH 6/7] fix deprecations

---
 ctd/plotting.py             |  2 +-
 ctd/read.py                 |  2 +-
 notebooks/quick_intro.ipynb | 10 +++++-----
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/ctd/plotting.py b/ctd/plotting.py
index 0aada6c..a8ec726 100644
--- a/ctd/plotting.py
+++ b/ctd/plotting.py
@@ -40,7 +40,7 @@ def plot_cast(df, secondary_y=False, label=None, ax=None, *args, **kwargs):
 
     if isinstance(df, pd.DataFrame):
         labels = label if label else df.columns
-        for k, (col, series) in enumerate(df.iteritems()):
+        for k, (col, series) in enumerate(df.items()):
             ax.plot(series, series.index, label=labels[k])
     elif isinstance(df, pd.Series):
         label = label if label else str(df.name)
diff --git a/ctd/read.py b/ctd/read.py
index c0544f5..9135cff 100644
--- a/ctd/read.py
+++ b/ctd/read.py
@@ -269,7 +269,7 @@ def from_btl(fname):
     df["Bottle"] = df["Bottle"].fillna(method="ffill")
     df["Date"] = df["Date"].fillna(method="ffill")
 
-    df["Statistic"] = df["Statistic"].str.replace(r"\(|\)", "")  # (avg) to avg
+    df["Statistic"] = df["Statistic"].str.lstrip("(").str.rstrip(")")  # (avg) to avg
 
     if "name" not in metadata:
         name = _basename(fname)[1]
diff --git a/notebooks/quick_intro.ipynb b/notebooks/quick_intro.ipynb
index 6d060b3..d28ca57 100644
--- a/notebooks/quick_intro.ipynb
+++ b/notebooks/quick_intro.ipynb
@@ -82,15 +82,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%matplotlib inline\n",
-    "\n",
     "from matplotlib import style\n",
     "\n",
-    "style.use(\"seaborn-whitegrid\")\n",
     "\n",
+    "style.use(\"seaborn-v0_8-whitegrid\")\n",
     "\n",
     "down[\"t090C\"].plot_cast()\n",
-    "down[\"c0S/m\"].plot_cast()"
+    "down[\"c0S/m\"].plot_cast();"
    ]
   },
   {
@@ -171,6 +169,7 @@
    "source": [
     "import matplotlib.pyplot as plt\n",
     "\n",
+    "\n",
     "fig, ax = plt.subplots()\n",
     "ax.plot(down.index, label=\"unfiltered\")\n",
     "ax.plot(down.lp_filter().index, label=\"filtered\")\n",
@@ -234,6 +233,7 @@
    "source": [
     "import gsw\n",
     "\n",
+    "\n",
     "p = proc.index\n",
     "\n",
     "SP = gsw.SP_from_C(proc[\"c0S/m\"].to_numpy() * 10.0, proc[\"t090C\"].to_numpy(), p)\n",
@@ -360,7 +360,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.4"
+   "version": "3.10.6"
   }
  },
  "nbformat": 4,

From 755c30c3b2b80a1e6745208c360a43b1ebfa1409 Mon Sep 17 00:00:00 2001
From: Filipe Fernandes <ocefpaf@gmail.com>
Date: Mon, 24 Oct 2022 16:05:40 -0300
Subject: [PATCH 7/7] fix URL

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index d81283a..11794b3 100644
--- a/README.md
+++ b/README.md
@@ -8,7 +8,7 @@
 Tools to load hydrographic data as pandas DataFrame with some handy methods for
 data pre-processing and analysis
 
-This module can load [SeaBird CTD (CNV)](https://www.seabird.com/software/SBEDataProcforWindows.htm),
+This module can load [SeaBird CTD (CNV)](https://www.seabird.com/),
 [Sippican XBT (EDF)](https://www.lockheedmartin.com/en-us/products/oceanographic-instrumentation.html),
 and [Falmouth CTD (ASCII)](https://www.falmouth.com/) formats.