Merge pull request #96 from ocefpaf/do_not_fail_without_pr

Author: ocefpaf

.isort.cfg

@@ -1,2 +1,2 @@
 [settings]
-known_third_party = matplotlib,numpy,pandas,pandas_flavor,pytest,setuptools
+known_third_party = gsw,matplotlib,numpy,pandas,pandas_flavor,pytest,setuptools

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v3.1.0
+  rev: v3.3.0
   hooks:
     - id: trailing-whitespace
       exclude: tests/data
@@ -14,46 +14,46 @@ repos:
       files: requirements-dev.txt
 
 - repo: https://github.com/econchick/interrogate
-  rev: 1.2.0
+  rev: 1.3.1
   hooks:
     - id: interrogate
       exclude: ^(docs|setup.py|tests)
       args: [--config=pyproject.toml]
 
 - repo: https://gitlab.com/pycqa/flake8
-  rev: 3.7.9
+  rev: 3.8.4
   hooks:
     - id: flake8
       exclude: docs/source/conf.py
-      args: [--max-line-length=105, --ignore=E203,E501,W503, --select=select=C,E,F,W,B,B950]
+      args: [--max-line-length=105, --ignore=E203]
 
 - repo: https://github.com/pre-commit/mirrors-isort
-  rev: v4.3.21
+  rev: v5.6.4
   hooks:
   - id: isort
     additional_dependencies: [toml]
     args: [--project=ctd, --multi-line=3, --lines-after-imports=2, --lines-between-types=1, --trailing-comma, --force-grid-wrap=0, --use-parentheses, --line-width=88]
 
 - repo: https://github.com/asottile/seed-isort-config
-  rev: v2.1.1
+  rev: v2.2.0
   hooks:
     - id: seed-isort-config
 
 - repo: https://github.com/psf/black
-  rev: stable
+  rev: 20.8b1
   hooks:
   - id: black
     language_version: python3
 
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v0.770
+  rev: v0.790
   hooks:
   - id: mypy
     exclude: docs/source/conf.py
     args: [--ignore-missing-imports]
 
 - repo: https://github.com/codespell-project/codespell
-  rev: v1.16.0
+  rev: v1.17.1
   hooks:
     - id: codespell
       args:

.travis.yml

@@ -28,17 +28,17 @@ matrix:
       env: PY=3
 
 before_install:
-  # Install miniconda and create TEST env.
+  # Install micromamba and create TEST env.
   - |
-    wget http://bit.ly/miniconda -O miniconda.sh
-    bash miniconda.sh -b -p $HOME/miniconda
-    export PATH="$HOME/miniconda/bin:$PATH"
-    conda config --set always_yes yes --set changeps1 no --set show_channel_urls true
-    conda update conda --quiet
-    conda config --add channels conda-forge --force
-    conda config --set channel_priority strict
-    conda create --name TEST python=$PY --file requirements.txt --file requirements-dev.txt
-    source activate TEST
+    wget -qO- https://micromamba.snakepit.net/api/micromamba/linux-64/latest | tar -xvj bin/micromamba --strip-components=1
+    ./micromamba shell init -s bash -p ~/micromamba
+    export MAMBA_ROOT_PREFIX=~/micromamba
+    export MAMBA_EXE=$(pwd)/micromamba
+    . ${MAMBA_ROOT_PREFIX}/etc/profile.d/mamba.sh
+
+    echo "micromamba version $(micromamba --version)"
+    micromamba create --yes --name TEST python=$PY pip --file requirements.txt --file requirements-dev.txt --channel conda-forge
+    micromamba activate TEST
 
 install:
   - pip install -e . --no-deps --force-reinstall
@@ -67,7 +67,8 @@ script:
   - |
     if [[ $TRAVIS_JOB_NAME == 'docs' ]]; then
       set -e
-      cp notebooks/quick_intro.ipynb docs/source/
+      travis_wait jupyter nbconvert --to notebook --execute notebooks/quick_intro.ipynb --output=quick_intro-output.ipynb
+      mv notebooks/quick_intro-output.ipynb docs/source/
       pushd docs
       make clean html linkcheck
       popd

ctd/extras.py

@@ -137,6 +137,7 @@ def gen_topomask(h, lon, lat, dx=1.0, kind="linear", plot=False):
     """
 
     import gsw
+
     from scipy.interpolate import interp1d
 
     h, lon, lat = list(map(np.asanyarray, (h, lon, lat)))
@@ -176,7 +177,8 @@ def plot_section(self, reverse=False, filled=False, **kw):
     labelsize = kw.pop("labelsize", 11)
     cmap = kw.pop("cmap", plt.cm.rainbow)
     levels = kw.pop(
-        "levels", np.arange(np.floor(data.min()), np.ceil(data.max()) + 0.5, 0.5),
+        "levels",
+        np.arange(np.floor(data.min()), np.ceil(data.max()) + 0.5, 0.5),
     )
 
     # Colorbar key words.
@@ -226,7 +228,14 @@ def plot_section(self, reverse=False, filled=False, **kw):
 
     # Color version.
     cs = ax.contourf(
-        x, z, data, cmap=cmap, levels=levels, alpha=1.0, extend=extend, zorder=2,
+        x,
+        z,
+        data,
+        cmap=cmap,
+        levels=levels,
+        alpha=1.0,
+        extend=extend,
+        zorder=2,
     )  # manual=True
     # Colorbar.
     cb = fig.colorbar(

ctd/read.py

@@ -14,6 +14,7 @@
 from io import StringIO
 from pathlib import Path
 
+import gsw
 import numpy as np
 import pandas as pd
 
@@ -390,12 +391,24 @@ def from_cnv(fname):
     )
     f.close()
 
-    prkeys = ["prM ", "prE", "prDM", "pr50M", "pr50M1", "prSM", "prdM", "pr"]
+    prkeys = ["prM ", "prE", "prDM", "pr50M", "pr50M1", "prSM", "prdM", "pr", "depSM"]
     prkey = [key for key in prkeys if key in df.columns]
     if len(prkey) != 1:
-        raise ValueError(f"Expected one pressure column, got {prkey}.")
+        raise ValueError(f"Expected one pressure/depth column, got {prkey}.")
     df.set_index(prkey, drop=True, inplace=True)
     df.index.name = "Pressure [dbar]"
+    if prkey == "depSM":
+        lat = metadata.get("lat", None)
+        if lat is not None:
+            df.index = gsw.p_from_z(
+                df.index, lat, geo_strf_dyn_height=0, sea_surface_geopotential=0
+            )
+        else:
+            warnings.war(
+                f"Missing latitude information. Cannot compute pressure! Your index is {prkey}, "
+                "please compute pressure manually with `gsw.p_from_z` and overwrite your index."
+            )
+            df.index.name = prkey
 
     name = _basename(fname)[1]
 

docs/source/conf.py

@@ -155,7 +155,13 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, "ctd.tex", "ctd Documentation", "Filipe Fernandes", "manual",)
+    (
+        master_doc,
+        "ctd.tex",
+        "ctd Documentation",
+        "Filipe Fernandes",
+        "manual",
+    )
 ]