docs and tests passing; some tweaks for new welly

docs/howto.rst

@@ -0,0 +1,14 @@
+How to...
+----------
+
+.. toctree::
+   :caption: How to...
+   :maxdepth: 1
+
+   tutorial/10_Extract_curves_into_striplogs.ipynb
+   tutorial/11_Parse_a_description_into_components.ipynb
+   tutorial/12_Calculate_sand_proportion.ipynb
+   tutorial/13_Work_with_binary_logs.ipynb
+   tutorial/14_Merge_overlapping_striplogs.ipynb
+   tutorial/15_Model_sequences_with_Markov_chains.ipynb
+   tutorial/16_Block_logs.ipynb

docs/index.rst

@@ -12,31 +12,18 @@ Striplog: Intervals of rocks and things
     | ``striplog`` facilitates the loading, processing, and analysis of striplogs and other sequential data in the subsurface (stratigraphy, chronostratigraphy, and so on). 
 
 
-Quick start
------------
-
-.. toctree::
-    :caption: Quick start
-
-Install ``striplog`` with pip:
-
-.. code-block:: shell
-
-    pip install striplog
-
-Carry on exploring with the user guide below.
-
-
 User guide
 ----------
 
 .. toctree::
    :caption: User guide
    :maxdepth: 2
-   :glob:
 
    installation
-   tutorial/*
+   tutorial/01_Basics.ipynb
+   tutorial/02_Basic_objects.ipynb
+   tutorial/03_Display_objects.ipynb
+   howto
 
 
 API reference

docs/tutorial/11_Parse_a_description_into_components.ipynb

@@ -0,0 +1 @@
+{"cells": [{"cell_type": "markdown", "metadata": {}, "source": ["# Parse a description into components\n", "\n", "This notebook requires at least version 0.8.8."]}, {"cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [{"data": {"text/plain": ["'0.8.8'"]}, "execution_count": 1, "metadata": {}, "output_type": "execute_result"}], "source": ["import striplog\n", "\n", "striplog.__version__"]}, {"cell_type": "markdown", "metadata": {}, "source": ["We have some text:"]}, {"cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [], "source": ["text = \"wet silty fine sand with tr clay\""]}, {"cell_type": "markdown", "metadata": {}, "source": ["To read this with `striplog`, we need to define a `Lexicon`. This is a dictionary-like object full of regular expressions, which acts as a bridge between this unstructured description and a dictionary-like `Component` object which `striplog` wants. The `Lexicon` also contains abbreviations for converting abbreviated text like cuttings descriptions into expanded words.\n", "\n", "A `Lexicon` to read only this text might look like:"]}, {"cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [], "source": ["from striplog import Lexicon\n", "\n", "lex_dict = {\n", "    'lithology': ['sand', 'clay'],\n", "    'grainsize': ['fine'],\n", "    'modifier':  ['silty'],\n", "    'amount':    ['trace'],\n", "    'moisture':  ['wet', 'dry'],\n", "    'abbreviations': {'tr': 'trace'},\n", "    'splitters': ['with'],\n", "    'parts_of_speech': {'noun': ['lithology'],\n", "                        'adjective': ['grainsize', 'modifier', 'moisture'],\n", "                        'subordinate': ['amount'],\n", "                       }\n", "}\n", "\n", "lexicon = Lexicon(lex_dict)"]}, {"cell_type": "markdown", "metadata": {}, "source": ["Now we can parse the text with it:"]}, {"cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [{"data": {"text/plain": ["[Component({'lithology': 'sand', 'grainsize': 'fine', 'modifier': 'silty', 'moisture': 'wet'}),\n", " Component({'lithology': 'clay', 'amount': 'trace'})]"]}, "execution_count": 4, "metadata": {}, "output_type": "execute_result"}], "source": ["from striplog import Interval\n", "\n", "Interval._parse_description(text, lexicon=lexicon, max_component=3, abbreviations=True)"]}, {"cell_type": "markdown", "metadata": {}, "source": ["But this is obviously a bit of a pain to make and maintain. So instead of definining a `Lexicon` from scratch, we'll modify the default one:"]}, {"cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [], "source": ["# Make and expand the lexicon.\n", "lexicon = Lexicon.default()\n", "\n", "# Add moisture words (or could add as other 'modifiers').\n", "lexicon.moisture = ['wet(?:tish)?', 'dry(?:ish)?']\n", "lexicon.parts_of_speech['adjective'] += ['moisture']\n", "\n", "# Add the comma as component splitter.\n", "lexicon.splitters += [', ']"]}, {"cell_type": "markdown", "metadata": {}, "source": ["Parsing with this yields the same results as before..."]}, {"cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [{"data": {"text/plain": ["[Component({'lithology': 'sand', 'modifier': 'silty', 'grainsize': 'fine', 'moisture': 'wet'}),\n", " Component({'lithology': 'clay'})]"]}, "execution_count": 6, "metadata": {}, "output_type": "execute_result"}], "source": ["Interval._parse_description(text, lexicon=lexicon, max_component=3)"]}, {"cell_type": "markdown", "metadata": {}, "source": ["...but we can parse more things now:"]}, {"cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [{"data": {"text/plain": ["[Component({'lithology': 'sandstone', 'grainsize': 'coarse'}),\n", " Component({'lithology': 'limestone', 'amount': 'minor'})]"]}, "execution_count": 7, "metadata": {}, "output_type": "execute_result"}], "source": ["Interval._parse_description(\"Coarse sandstone with minor limestone\", lexicon=lexicon, max_component=3)"]}, {"cell_type": "markdown", "metadata": {}, "source": ["`striplog` does all this parsing internally when you use the `Striplog.from_descriptions()` class method.\n", "\n", "Have fun!"]}], "metadata": {"kernelspec": {"display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3"}, "language_info": {"codemirror_mode": {"name": "ipython", "version": 3}, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.9.7"}}, "nbformat": 4, "nbformat_minor": 4}

docs/tutorial/og815.csv

@@ -0,0 +1,51 @@
+,Wells,Date,Type,Top,Bottom
+1,OG-815,1972-10-21,perforation,2426,2431
+2,OG-815,1972-10-30,perforation,2431,2439
+0,OG-815,1972-11-04,perforation,2258,2270
+3,OG-815,1972-11-04,perforation,2369,2374
+4,OG-815,1976-05-25,perforation,2352,2362
+6,OG-815,1976-05-25,squeeze,2369,2374
+5,OG-815,1976-05-28,perforation,2344,2348
+7,OG-815,1976-05-28,squeeze,2352,2362
+8,OG-815,1976-05-28,squeeze,2344,2348
+9,OG-815,1976-06-02,perforation,2310,2320
+10,OG-815,1998-02-21,perforation,2310,2320
+12,OG-815,1998-02-22,squeeze,2258,2270
+11,OG-815,1998-02-22,perforation,2292,2298
+13,OG-815,2000-11-18,squeeze,2310,2320
+14,OG-815,2000-11-18,squeeze,2292,2298
+15,OG-815,2001-05-21,perforation,2260,2270
+16,OG-815,2001-05-21,perforation,2246,2250
+17,OG-815,2002-05-26,perforation,2192,2195
+18,OG-815,2002-05-27,perforation,2185,2192
+19,OG-815,2002-05-30,welltest-pm,2246,2250
+20,OG-815,2002-05-30,welltest-pm,2260,2270
+21,OG-815,2002-05-30,welltest-pm,2292,2298
+22,OG-815,2002-05-30,welltest-pm,2310,2320
+27,OG-815,2002-06-03,squeeze,2310,2320
+26,OG-815,2002-06-03,squeeze,2292,2298
+24,OG-815,2002-06-03,squeeze,2246,2250
+23,OG-815,2002-06-03,perforation,2185,2189
+25,OG-815,2002-06-03,squeeze,2260,2270
+28,OG-815,2002-06-05,perforation,2132,2141
+29,OG-815,2006-07-18,perforation,2255,2263
+30,OG-815,2006-07-19,perforation,2263,2266
+31,OG-815,2006-07-19,perforation,2243,2246
+32,OG-815,2008-04-28,perforation,2119,2127
+33,OG-815,2008-04-28,perforation,2112,2119
+34,OG-815,2008-04-28,squeeze,2255,2266
+35,OG-815,2008-04-28,squeeze,2243,2246
+36,OG-815,2008-06-22,perforation,2100,2105
+37,OG-815,2008-06-23,perforation,1992,2005
+38,OG-815,2008-06-24,perforation,1986,1992
+39,OG-815,2009-10-23,perforation,2037,2053
+40,OG-815,2009-10-23,perforation,2018,2023
+41,OG-815,2012-05-29,perforation,2243,2245
+42,OG-815,2012-05-30,perforation,2183,2190
+43,OG-815,2012-05-30,perforation,2132,2136
+44,OG-815,2012-05-30,perforation,1995,2005
+45,OG-815,2015-11-13,perforation,2189,2195
+46,OG-815,2015-11-14,perforation,2180,2189
+47,OG-815,2015-11-14,perforation,1995,2005
+48,OG-815,2018-07-31,perforation,2100,2105
+49,OG-815,2018-07-31,perforation,2000,2010