shipgrav 1.0.0__py2.py3-none-any.whl → 1.0.3__py2.py3-none-any.whl

shipgrav/__init__.py

@@ -9,7 +9,11 @@ DGS gravimeters output two types of files: serial, or 'raw' files; and 'laptop'
 Installation
 ------------
 
-shipgrav can be installed from the source files (`available on github <https://github.com/PFPE/shipgrav>`_) using ``pip``.
+shipgrav can be installed from `PyPI <https://pypi.org/project/shipgrav/>`_ using ``pip``. we recommend using an environment management tool like `conda <https://anaconda.org>`_. An exemplary set of commands to make a conda enviroment with shipgrav would be: ::
+
+    conda create --name shipgrav numpy scipy pandas statsmodels tomli pyyaml matplotlib geographiclib
+    conda activate shipgrav
+    pip install shipgrav
 
 shipgrav's dependencies are
 
@@ -21,15 +25,9 @@ shipgrav's dependencies are
 * tomli
 * pyyaml
 * matplotlib (optional, needed to run some of the example scripts)
+* geographiclib (optional, needed to run one of the example scripts)
 
-To install shipgrav, we recommend using an environment management tool like `conda <https://anaconda.org>`_. An exemplary set of commands to make a conda enviroment with shipgrav would be: ::
-
-    conda create --name shipgrav numpy scipy pandas statsmodels tomli pyyaml matplotlib
-    conda activate shipgrav
-    cd /path/to/put/source/files
-    git clone https://github.com/PFPE/shipgrav.git
-    cd shipgrav/
-    pip install .
+The example scripts are `available on github <https://github.com/PFPE/shipgrav>`_. They are not packaged with the PyPI package and must be downloaded separately.
 
 Modules and files
 -----------------
@@ -144,4 +142,6 @@ Contributing
 
 Do you have ideas for making this software better? Go ahead and `raise an issue <https://github.com/PFPE/shipgrav/issues>`_ on the github page or, if you're a savvy Python programmer, submit a pull request. You can also email PFPE at pfpe-interal(at)whoi.edu.
 
+If you raise an issue on github, please include as much detail as possible, such as the text of error messages. If there are no visible errors but you think the code is behaving oddly, provide a description of what the code is doing and what you think it *should* be doing instead. PFPE may ask for additional details or copies of data files in order to reproduce and diagnose an issue.
+
 """

shipgrav/io.py

@@ -169,7 +169,7 @@ def _navdate_Atlantis(allnav, talker):
 
     for i in range(N):
         pre = subnav[i].split(talker)[0]
-        date = re.findall('NAV (\d{4})/(\d{2})/(\d{2})', pre)[0]
+        date = re.findall(r'NAV (\d{4})/(\d{2})/(\d{2})', pre)[0]
         year = int(date[0])  # year
         mon = int(date[1])  # month
         day = int(date[2])  # day
@@ -191,7 +191,7 @@ def _navdate_NBP(allnav, talker):
 
     for i in range(N):
         pre = subnav[i].split(talker)[0]
-        date = re.findall('(\d{2})\+(\d{2,3}):.*', pre)[0]
+        date = re.findall(r'(\d{2})\+(\d{2,3}):.*', pre)[0]
         # year (NBP didn't exist before 2000 so this is ok)
         year = '20' + date[0]
         doy = date[1]  # doy
@@ -216,7 +216,7 @@ def _navdate_Thompson(allnav, talker):
 
     for i in range(N):
         pre = subnav[i].split(talker)[0]
-        date = re.findall('(\d{2})/(\d{2})/(\d{4}),*', pre)[0]
+        date = re.findall(r'(\d{2})/(\d{2})/(\d{4}),*', pre)[0]
         year = int(date[2])
         mon = int(date[0])
         day = int(date[1])
@@ -247,8 +247,8 @@ def _navdate_Revelle(allnav, talker):
         for k in range(inds[i]-1, j, -1):  # step backwards toward the last talker line
             before = allnav[k]
             # date is at the start of this line
-            if re.match('(\d{4})-(\d{2})-(\d{2})T*', before):
-                date = re.findall('(\d{4})-(\d{2})-(\d{2})T*', before)[0]
+            if re.match(r'(\d{4})-(\d{2})-(\d{2})T*', before):
+                date = re.findall(r'(\d{4})-(\d{2})-(\d{2})T*', before)[0]
                 year = int(date[0])
                 mon = int(date[1])
                 day = int(date[2])
@@ -269,12 +269,12 @@ def _navdate_Ride(allnav, talker):
 
     for i in range(N):
         if talker == 'INGGA':  # on Ride, uses posix timestamps
-            date = re.findall('(\d+(\.\d*)?) \$%s' % talker, subnav[i])[0]
+            date = re.findall(r'(\d+(\.\d*)?) \$%s' % talker, subnav[i])[0]
             timest[i] = datetime.fromtimestamp(
                 float(date[0]), tzinfo=timezone.utc)
         elif talker == 'GPGGA':  # includes time only with date, unlike other GPGGAs
             date = re.findall(
-                '(\d{4})\-(\d{2})\-(\d{2})T(\d{2}):(\d{2}):(\d{2})\.(\d.*?)Z', subnav[i])[0]
+                r'(\d{4})\-(\d{2})\-(\d{2})T(\d{2}):(\d{2}):(\d{2})\.(\d.*?)Z', subnav[i])[0]
             year = int(date[0])
             mon = int(date[1])
             day = int(date[2])
@@ -383,9 +383,8 @@ def read_bgm_rgs(fp, ship):
     dats = []
     for path in fp:
         dat = pd.read_csv(path, delimiter=' ', names=['date', 'time', 'grav', 'lat', 'lon'],
-                          usecols=(1, 2, 3, 11, 12), parse_dates=[[0, 1]])
-        ndt = [e.tz_localize(timezone.utc) for e in dat['date_time']]
-        dat['date_time'] = ndt
+                          usecols=(1, 2, 3, 11, 12))
+        dat['date_time'] = pd.to_datetime(dat.pop('date')+' '+dat.pop('time'),utc=True)
         dats.append(dat)
 
     return pd.concat(dats, ignore_index=True)
@@ -456,10 +455,8 @@ def _bgmserial_Atlantis(path):
     def count(x): return (
         int(x.split(':')[-1]))  # function to parse counts column
     dat = pd.read_csv(path, delimiter=' ', names=['date', 'time', 'counts'], usecols=(1, 2, 4),
-                      parse_dates=[[0, 1]], converters={'counts': count})
-    ndt = [e.tz_localize(timezone.utc)
-           for e in dat['date_time']]  # timestamps cannot be naive
-    dat['date_time'] = ndt
+                      converters={'counts': count})
+    dat['date_time'] = pd.to_datetime(dat.pop('date')+' '+dat.pop('time'),utc=True)
     return dat
 
 
@@ -468,9 +465,8 @@ def _bgmserial_Thompson(path):
     """
     def count(x): return (int(x.split(' ')[0].split(':')[-1]))
     dat = pd.read_csv(path, delimiter=',', names=['date', 'time', 'counts'],
-                      parse_dates=[[0, 1]], converters={'counts': count})
-    ndt = [e.tz_localize(timezone.utc) for e in dat['date_time']]
-    dat['date_time'] = ndt
+                    converters={'counts': count})
+    dat['date_time'] = pd.to_datetime(dat.pop('date')+' '+dat.pop('time'),utc=True)
     return dat
 
 
@@ -575,10 +571,8 @@ def _dgs_laptop_Thompson(path):
     """
     dat = pd.read_csv(path, delimiter=',', names=['date', 'time', 'rgrav', 've', 'vcc',
                                                   'al', 'ax', 'lat', 'lon'],
-                      usecols=(0, 1, 3, 12, 13, 14, 15, 16, 17),
-                      parse_dates=[[0, 1]])
-    ndt = [e.tz_localize(timezone.utc) for e in dat['date_time']]
-    dat['date_time'] = ndt
+                      usecols=(0, 1, 3, 12, 13, 14, 15, 16, 17))
+    dat['date_time'] = pd.to_datetime(dat.pop('date')+' '+dat.pop('time'),utc=True)
     return dat
 
 
@@ -746,4 +740,13 @@ def read_other_stuff(yaml_file, data_file, tag):
         except KeyError:
             pass
 
-    return df.apply(pd.to_numeric, errors='ignore'), col_info
+    def numeric(col):
+        try:
+            return pd.to_numeric(col)
+        except:
+            return col
+
+    for ckey in df.columns:     # to_numeric by column so errors for datetimes are skipped
+        df[ckey] = df[ckey].apply(numeric)  # slower than applying to whole df, but avoids errors
+
+    return df, col_info

shipgrav/tests/__init__.py

@@ -2,15 +2,16 @@
 Tests for shipgrav
 """
 
-from pkg_resources import resource_filename
 import sys
 import unittest
+import importlib.resources as importlib_resources
 
 
 def run():
     loader = unittest.TestLoader()
-    test_dir = resource_filename('shipgrav', 'tests')
-    suite = loader.discover(test_dir)
+    ref = importlib_resources.files('shipgrav') / 'tests'
+    with importlib_resources.as_file(ref) as path:
+        suite = loader.discover(ref)
     runner = unittest.runner.TextTestRunner()  # verbosity=2)
     ret = not runner.run(suite).wasSuccessful()
     sys.exit(ret)

{shipgrav-1.0.0.dist-info → shipgrav-1.0.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: shipgrav
-Version: 1.0.0
+Version: 1.0.3
 Summary: Functions for marine gravity data processing and reduction
 Author-email: "Hannah F. Mark" <hmark@whoi.edu>
 Maintainer-email: "Hannah F. Mark" <hmark@whoi.edu>
@@ -9,13 +9,15 @@ Keywords: UNOLS,gravimetry,marine gravity
 Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
-Requires-Dist: matplotlib
 Requires-Dist: numpy
 Requires-Dist: pandas
 Requires-Dist: pyyaml
 Requires-Dist: scipy
 Requires-Dist: statsmodels
 Requires-Dist: tomli
+Provides-Extra: examples
+Requires-Dist: geographiclib; extra == 'examples'
+Requires-Dist: matplotlib; extra == 'examples'
 Description-Content-Type: text/markdown
 
 # shipgrav
@@ -35,10 +37,14 @@ pyyaml
 To run the example scripts, you will also need matplotlib.
 
 ## Installation
-shipgrav can be installed using `pip`. Detailed instructions are in the [documentation](https://shipgrav.readthedocs.io/).
+shipgrav can be installed from PyPI using `pip`. Detailed instructions are in the [documentation](https://shipgrav.readthedocs.io/).
 
 ## Documentation and usage
 The shipgrav documentation is available online at [shipgrav.readthedocs.io](https://shipgrav.readthedocs.io/). It can also be accessed offline by building the contents of the `docs` folder using sphinx.
 
 ## Contributing to shipgrav
 Please do! If you have ideas for how to make shipgrav better, you can raise an issue on github or contact PFPE.
+
+If you raise an issue on github, please include as much detail as possible about any errors you are encountering or any proposed enhancements to the code. Include the text of any error messages, and if the issue is unexpected behavior from the code without any visible error messages, describe both what the code is doing and what you think it *should* be doing instead. PFPE may ask for additional details and/or copies of data files in order to reproduce and diagnose an issue.
+
+Additions or enhancements to the code are also welcome. Contributors are invited to fork the repository and submit pull requests for the maintainers to review.

{shipgrav-1.0.0.dist-info → shipgrav-1.0.3.dist-info}/RECORD

@@ -1,10 +1,10 @@
-shipgrav/__init__.py,sha256=oLzfXDKCuKsg3qHtE7Pg_8sxUkavmlfn1VkN5J36nWQ,11043
+shipgrav/__init__.py,sha256=VUDa7_eQMngYnvi0059W2Il7BVUWT2QoNHud6962xB4,11529
 shipgrav/database.toml,sha256=qRSZBRsoMsbyhjkaYlXsWtVDz3JAhoW-cYfSoo8U3K4,532
 shipgrav/grav.py,sha256=OQK2HNiZtLlycjVwidpD902K08NaWbZXnjZSbjyPF8I,43410
-shipgrav/io.py,sha256=j9uy5z-CqhkUN4T-3iW5o5-cRLgjoGwfNc4o7cjw_pA,29273
+shipgrav/io.py,sha256=vCSyE2q4Dp4H-mqpg1xWuVu_bpeI0x5o1KXUq3kYsiE,29352
 shipgrav/nav.py,sha256=3E2Il-PhTEPVv8_8PrLVe7h6slHq-2HYX_Q8PdpB6X4,2895
 shipgrav/utils.py,sha256=h5gd8cnWlO1pyAqLkJIVrbFRRLbZzHj-xJ9pWchaHtI,9521
-shipgrav/tests/__init__.py,sha256=mejp00TQif0WLU45j40zfBQXN2RujaOP6ZSTgxUm4A8,367
+shipgrav/tests/__init__.py,sha256=ljlA5qi9b7PQCzxzlNRc1QdGvA9A2mv66z53kNLSL44,427
 shipgrav/tests/__main__.py,sha256=iJ8xSU8ucCmIDcOuv8uasZ9iV5dNR0DDuFRZrG0o2hE,38
 shipgrav/tests/test_grav_data.py,sha256=OnPNW8XIG3DvWOr_trQY71XLzA0rff8VfGd4Az3B37Q,3403
 shipgrav/tests/test_grav_nodata.py,sha256=0z5KUTzT9cJPko_bhyDG4EFm4i5xgOdVhJVKU2cPxX8,1493
@@ -18,7 +18,7 @@ shipgrav/tests/ex_files/SR2312_dgs_raw.txt,sha256=rTlIn75MBICBjnkjcn9SPCwpC5J3lM
 shipgrav/tests/ex_files/SR2312_mru.txt,sha256=YBM4qy4BS_D0U4ngEyoIFZr4QQbMWQgEO681fVEmgYM,1060
 shipgrav/tests/ex_files/TN400_bgm.Raw,sha256=DL7T2aJednjGLMKJo6K8KcUYLMjQCiv6bsUiczlVwKw,74
 shipgrav/tests/ex_files/TN400_nav.Raw,sha256=66dgRQTXjf0JItMWE1ZGUO6NptrGqV6JyN2wdYe5bW8,194
-shipgrav-1.0.0.dist-info/METADATA,sha256=Ou01ttXgo18YQDfv2EngjSm-paE81HEqzkZN2Fd7H8A,1745
-shipgrav-1.0.0.dist-info/WHEEL,sha256=fl6v0VwpzfGBVsGtkAkhILUlJxROXbA3HvRL6Fe3140,105
-shipgrav-1.0.0.dist-info/licenses/LICENSE,sha256=5X8cMguM-HmKfS_4Om-eBqM6A1hfbgZf6pfx2G24QFI,35150
-shipgrav-1.0.0.dist-info/RECORD,,
+shipgrav-1.0.3.dist-info/METADATA,sha256=IS9pbX283aH8u4XToZXBq3u9CRAIhuLXVj-GSfRsg-k,2493
+shipgrav-1.0.3.dist-info/WHEEL,sha256=fl6v0VwpzfGBVsGtkAkhILUlJxROXbA3HvRL6Fe3140,105
+shipgrav-1.0.3.dist-info/licenses/LICENSE,sha256=5X8cMguM-HmKfS_4Om-eBqM6A1hfbgZf6pfx2G24QFI,35150
+shipgrav-1.0.3.dist-info/RECORD,,