More on docs and minor refactor

docs/index.rst

@@ -32,8 +32,10 @@ Modules and Classes
 .. toctree::
     :maxdepth: 2
 
-    metadata <metadata/index>
     utils <utils/index>
+    metadata <metadata/index>
+    jobs <jobs/index>
+
 
 
 

docs/jobs/index.rst

@@ -0,0 +1,10 @@
+
+jobs
+====
+
+.. toctree::
+    :maxdepth: 1
+
+    Pipeline <pipeline>
+
+

docs/jobs/pipeline.rst

@@ -0,0 +1,7 @@
+
+Pipeline
+========
+
+.. autoclass:: emtools.jobs.Pipeline
+   :members:
+

docs/metadata/starfile.rst

@@ -50,9 +50,11 @@ that parsing rows if not needed. These methods will also create an index of wher
 data blocks are in the file, so if you need to read a data table, it will jump to
 that position in the file.
 
+Reading a Table
+---------------
 
-Iterating over the rows
------------------------
+Iterating over the Table rows
+-----------------------------
 
 In some cases, we just want to iterate over the rows and operate on them one by one.
 In that case, it is not necessary to fully load the whole table in memory. Iteration

docs/utils/index.rst

@@ -5,5 +5,7 @@ utils
 .. toctree::
     :maxdepth: 1
 
-    Color, Timer <misc>
-    Process <process>
+    Color, Pretty, Timer <misc>
+    Process, Path, System <process>
+
+

docs/utils/misc.rst

@@ -1,10 +1,18 @@
 
-Color, Pretty
-=============
+Color
+=====
 
 .. autoclass:: emtools.utils.Color
    :members:
 
+Pretty
+======
+
 .. autoclass:: emtools.utils.Pretty
    :members:
 
+Timer
+=====
+
+.. autoclass:: emtools.utils.Timer
+   :members:

docs/utils/process.rst

@@ -2,13 +2,18 @@
 Process
 =======
 
+.. autoclass:: emtools.utils.Process
+   :members:
 
+Path
+====
 
-Reference
----------
-
-.. autoclass:: emtools.utils.Process
+.. autoclass:: emtools.utils.Path
    :members:
 
+System
+======
 
+.. autoclass:: emtools.utils.System
+   :members:
 

emtools/processing/__init__.py → emtools/jobs/__init__.py

@@ -14,3 +14,6 @@
 # *
 # **************************************************************************
 
+from .pipeline import Pipeline
+
+__all__ = ["Pipeline"]

emtools/utils/__init__.py

@@ -15,15 +15,16 @@
 # **************************************************************************
 
 from .color import Color
-from .process import Process
 from .pretty import Pretty
-from .path import Path
 from .time import Timer
-from .pipeline import Pipeline
+
+from .process import Process
+from .path import Path
 from .system import System
+
 from .server import JsonTCPServer, JsonTCPClient
 
 
-__all__ = [Color, Process, Pretty, Path, Timer, Pipeline, System,
-           JsonTCPServer, JsonTCPClient]
+__all__ = ["Color", "Pretty", "Timer", "Process", "Path", "System",
+           "JsonTCPServer", "JsonTCPClient"]
 

emtools/utils/color.py

@@ -26,6 +26,9 @@
 
 
 class Color:
+    """ Basic helper class to have colored string.
+    Useful for commands and log messages. """
+
     @staticmethod
     def green(msg):
         return f'{OKGREEN}{msg}{ENDC}'

emtools/utils/path.py

@@ -1,15 +1,11 @@
 
 import os
 import time
-from glob import glob
 from datetime import datetime as dt
-from datetime import timedelta
 from collections import OrderedDict
-import numpy as np
 
 from .pretty import Pretty
 from .process import Process
-from .color import Color
 
 
 class Path:
@@ -149,7 +145,7 @@ def _mkdir(d):
     @staticmethod
     def replaceExt(filename, newExt):
         """ Replace the current path extension(from last .)
-        with a new one. The new one should not contains the ."""
+        with a new one. The new one should not contain the ."""
         return Path.removeExt(filename) + '.' + newExt
 
     @staticmethod

emtools/utils/pretty.py

@@ -20,6 +20,9 @@
 
 
 class Pretty:
+    """ Helper class for "pretty" string formatting from several input types
+    (e.g. size, dates, timestamps, elapsed, etc.).
+    """
     # Default timestamp
     DATETIME_FORMAT = '%Y-%m-%d %H:%M:%S'
     DATE_FORMAT = '%Y-%m-%d'

emtools/utils/system.py

@@ -23,6 +23,7 @@
 import socket
 import platform
 import psutil
+
 from .process import Process
 
 
@@ -33,6 +34,7 @@ class System:
 
     @staticmethod
     def gpus():
+        """ Return a dictionary with existing GPUs and their properties. """
         gpus = []
         query = Process(System.NVIDIA_SMI_QUERY[0],
                         *System.NVIDIA_SMI_QUERY[1:], doRaise=False)
@@ -69,6 +71,7 @@ def cpus():
 
     @staticmethod
     def memory():
+        """ Return the total virtual memory of the system. (in Gb) """
         return psutil.virtual_memory().total // (1024 * 1024 * 1024)  # GiB
 
     @staticmethod
@@ -92,4 +95,5 @@ def specs():
 
     @staticmethod
     def hostname():
+        """ Return the hostname. """
         return socket.gethostname()