Add --D48 to CLI

mdaeron · Jul 20, 2023 · 12b3b7b · 12b3b7b
1 parent a541e62
commit 12b3b7b
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diff --git a/D47crunch/__init__.py b/D47crunch/__init__.py
@@ -22,7 +22,7 @@
 __copyright__ = 'Copyright (c) 2023 Mathieu Daëron'
 __license__   = 'Modified BSD License - https://opensource.org/licenses/BSD-3-Clause'
 __date__      = '2023-07-20'
-__version__   = '2.2.0'
+__version__   = '2.2.1'
 
 import os
 import numpy as np
@@ -3249,6 +3249,7 @@ def _cli(
 	exclude: Annotated[str, typer.Option('--exclude', '-e', help = 'The path of a file specifying UIDs and/or Samples to exclude')] = 'none',
 	anchors: Annotated[str, typer.Option('--anchors', '-a', help = 'The path of a file specifying custom anchors')] = 'none',
 	output_dir: Annotated[str, typer.Option('--output-dir', '-o', help = 'Specify the output directory')] = 'output',
+	run_D48: Annotated[bool, typer.Option('--D48', help = 'Also standardize D48')] = False,
 	):
 	"""
 	Process raw D47 data and return standardized results.
@@ -3290,13 +3291,51 @@ def _cli(
 	data.crunch()
 	data.standardize()
 	data.summary(dir = output_dir)
-	data.table_of_samples(dir = output_dir)
-	data.table_of_sessions(dir = output_dir)
-	data.plot_sessions(dir = output_dir)
 	data.plot_residuals(dir = output_dir, filename = 'D47_residuals.pdf', kde = True)
-	data.table_of_analyses(dir = output_dir)
-	data.plot_distribution_of_analyses(dir = output_dir)
 	data.plot_bulk_compositions(dir = output_dir + '/bulk_compositions')
+	data.plot_sessions(dir = output_dir)
+
+	if not run_D48:
+		data.table_of_samples(dir = output_dir)
+		data.table_of_analyses(dir = output_dir)
+		data.table_of_sessions(dir = output_dir)
+
+
+	if run_D48:
+		data2 = D48data()
+		data2.read(rawdata)
+
+		data2 = D48data([r for r in data2 if r['UID'] not in exclude_uid and r['Sample'] not in exclude_sample])
 
+		if anchors != 'none':
+			data2.Nominal_d13C_VPDB = {
+				_['Sample']: _['d13C_VPDB']
+				for _ in anchors
+				if 'd13C_VPDB' in _
+				}
+			data2.Nominal_d18O_VPDB = {
+				_['Sample']: _['d18O_VPDB']
+				for _ in anchors
+				if 'd18O_VPDB' in _
+				}
+			data2.Nominal_D4x = {
+				_['Sample']: _['D48']
+				for _ in anchors
+				if 'D48' in _
+				}
+
+		data2.refresh()
+		data2.wg()
+		data2.crunch()
+		data2.standardize()
+		data2.summary(dir = output_dir)
+		data2.plot_sessions(dir = output_dir)
+		data2.plot_residuals(dir = output_dir, filename = 'D48_residuals.pdf', kde = True)
+		data2.plot_distribution_of_analyses(dir = output_dir)
+
+		table_of_analyses(data, data2, dir = output_dir)
+		table_of_samples(data, data2, dir = output_dir)
+		table_of_sessions(data, data2, dir = output_dir)
+
 def __cli():
 	_app()
diff --git a/changelog.md b/changelog.md
@@ -1,5 +1,13 @@
 # Changelog
 
+## v2.2.1
+*Released on 2023-07-20*
+
+### New feature
+
+* The CLI now processes Δ48 as well as Δ47 data, thanks to the `--D48` option.
+
+
 ## v2.2.0
 *Released on 2023-07-20*
 

diff --git a/code_examples/virtual_data/output.txt b/code_examples/virtual_data/output.txt
diff --git a/docs/D47_plot_Session_01.png b/docs/D47_plot_Session_01.png
diff --git a/docs/D47_plot_Session_02.png b/docs/D47_plot_Session_02.png
diff --git a/docs/D47_plot_Session_03.png b/docs/D47_plot_Session_03.png
diff --git a/docs/D47_plot_Session_04.png b/docs/D47_plot_Session_04.png
diff --git a/docs/D47_plot_Session_05.png b/docs/D47_plot_Session_05.png
diff --git a/docs/D47_plot_Session_06.png b/docs/D47_plot_Session_06.png
diff --git a/docs/D47_plot_Session_07.png b/docs/D47_plot_Session_07.png
diff --git a/docs/D47_plot_Session_08.png b/docs/D47_plot_Session_08.png
diff --git a/docs/D47_plot_Session_09.png b/docs/D47_plot_Session_09.png
diff --git a/docs/D47_plot_Session_10.png b/docs/D47_plot_Session_10.png
diff --git a/docs/cli.md b/docs/cli.md
@@ -1,6 +1,6 @@
 # 3. Command-Line Interface (CLI)
 
-Instead of writing Python code, you may directly use the CLI to process raw D47 data using reasonable defaults. The simplest way is simply to call
+Instead of writing Python code, you may directly use the CLI to process raw Δ47 and Δ48 data using reasonable defaults. The simplest way is simply to call:
 
 ```txt
 D47crunch rawdata.csv
@@ -62,3 +62,5 @@ The `--output-dir` or `-o` option may be used to specify a custom directory name
 ```txt
 D47crunch -o `date "+%Y-%M-%d-%Hh%M"` rawdata.csv
 ```
+
+To process Δ48 as well as Δ47, just add the `--D48` option.
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/residuals.png b/docs/residuals.png
diff --git a/docs/time_distribution.png b/docs/time_distribution.png
diff --git a/readme.md b/readme.md
@@ -4,7 +4,7 @@
 
 Python library for processing and standardizing carbonate clumped-isotope analyses, from low-level data out of a dual-inlet mass spectrometer to final, “absolute” Δ<sub>47</sub> and Δ<sub>48</sub> values with fully propagated analytical error estimates.
 
-This also provides a command-line interface making it possible to process a multi-session Δ<sub>47</sub> dataset by simply calling `D47crunch rawdata.csv`. See the [CLI documentation](https://mdaeron.github.io/D47crunch/#3-command-line-interface-cli) for more options.
+This also provides a command-line interface making it possible to process a multi-session Δ<sub>47</sub> (and potentially Δ<sub>48</sub>) dataset by simply calling `D47crunch rawdata.csv`. See the [CLI documentation](https://mdaeron.github.io/D47crunch/#3-command-line-interface-cli) for more options.
 
 ## Documentation