Merge pull request #13 from Hekstra-Lab/docs

Update the README

README.md

@@ -1,2 +1,66 @@
 # efxtools
-Useful scripts for EFX analysis
+Efxtools contains scripts for some important diffraction data analysis tasks. 
+
+
+### Installation
+
+For users who don't want to [configure ssh access](https://docs.github.com/en/authentication/connecting-to-github-with-ssh/adding-a-new-ssh-key-to-your-github-account) to GitHub, 
+you may install from source without git with the following steps. 
+
+ 1) [download the latest source code](https://github.com/Hekstra-Lab/efxtools/archive/refs/heads/main.zip)
+ 2) Unpack the `.zip` file from (1) using your system's archive tool. You may do this in the file browser on most modern operating systems. 
+ 3) In a terminal, navigate to the extracted source code directory (for instance `cd /home/user/efxtools-main`).
+ 4) Type `python setup.py install` or `pip install -e .`. Use the latter if you would like to modify the source code in the future. 
+
+### Design and usage
+
+Efxtools is designed primarily as a command line interface. 
+Applications from this package are prefixed with `efxtools.`.
+
+Users can **list available commands** by typing `efxtools.` and double-pressing the `TAB` key. 
+Each subprogram is documented using the [argparse library](https://docs.python.org/3/library/argparse.html).
+To get usage info for a subprogram, use the `-h` or `--help` flag. 
+For instance,
+
+```bash
+$ efxtools.find_peaks -h
+```
+
+will print the following
+
+```bash
+usage: efxtools.find_peaks [-h] -f STRUCTURE_FACTOR_KEY -p PHASE_KEY [-o CSV_OUT] [-z SIGMA_CUTOFF] [-w WEIGHT_KEY] [--sample-rate SAMPLE_RATE] [--min-volume MIN_VOLUME]
+                           [--min-score MIN_SCORE] [--min-peak MIN_PEAK] [-d DISTANCE_CUTOFF] [--use-long-names]
+                           mtz_file pdb_file
+
+Search an electron density map for peaks in the vicinity of a structure.
+
+positional arguments:
+  mtz_file
+  pdb_file
+
+options:
+  -h, --help            show this help message and exit
+  -f STRUCTURE_FACTOR_KEY, --structure-factor-key STRUCTURE_FACTOR_KEY
+                        column label of the structure factor you want to use.
+  -p PHASE_KEY, --phase-key PHASE_KEY
+                        column label of the phase you want to use.
+  -o CSV_OUT, --csv-out CSV_OUT
+                        output the report to a csv file
+  -z SIGMA_CUTOFF, --sigma-cutoff SIGMA_CUTOFF
+                        the z-score cutoff for voxels to be included in the peak search. the default is 1.5
+  -w WEIGHT_KEY, --weight-key WEIGHT_KEY
+                        column label of any weights you wish to apply to the map.
+  --sample-rate SAMPLE_RATE
+                        change fft oversampling from the default (3).
+  --min-volume MIN_VOLUME
+                        the minimum volume of peaks with default zero.
+  --min-score MIN_SCORE
+                        the minimum score of peaks with default zero.
+  --min-peak MIN_PEAK   the minimum peak value with default zero.
+  -d DISTANCE_CUTOFF, --distance-cutoff DISTANCE_CUTOFF
+                        the distance cutoff of nearest neighbor search with default of 4 angstroms.
+  --use-long-names      use more verbose column names in the peak report.
+
+```
+