Fleshed out the README.

README.md

@@ -12,6 +12,107 @@
 
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-# SewerRat
+# Python interface to the SewerRat API
 
-Python interface to the [SewerRat](https://github.com/ArtifactDB/SewerRat) API.
+## Overview
+
+The **sewerrat** package implements an R client for the [API of the same name](https://github.com/ArtifactDB/SewerRat).
+This allows users to easily query the SewerRat search index, register or deregister their own directories in the index, and quickly save and load Bioconductor objects for registration.
+It is assumed that the users of the **sewerrat** client and the SewerRat API itself are accessing the same shared filesystem;
+this is typically the case for high-performance computing (HPC) clusters in scientific institutions.
+
+## Registering directories
+
+Let's mock up a directory of metadata files:
+
+```python
+import tempfile
+import os
+
+mydir = tempfile.mkdtemp()
+with open(os.path.join(mydir, "metadata.json"), "w") as handle:
+    handle.write('{ "first": "foo", "last": "bar" }')
+
+os.mkdir(os.path.join(mydir, "diet"))
+with open(os.path.join(mydir, "diet", "metadata.json"), "w") as handle:
+    handle.write('{ "fish": "barramundi" }')
+```
+
+We can then easily register it:
+
+```python
+import sewerrat
+
+# Only indexing metadata files named 'metadata.json'.
+sewerrat.register(mydir, names=["metadata.json"])
+```
+
+Similarly, we can deregister this directory with `deregister(mydir)`.
+
+## Searching the index
+
+Use the `query()` function to perform free-text searches:
+
+```python
+sewerrat.query("foo")
+sewerrat.query("bar%") # partial match to 'bar...'
+sewerrat.query("bar% AND foo") # boolean operations
+sewerrat.query("fish:bar%") # match in the 'fish' field
+```
+
+We can also search on the user, path components, and time of creation:
+
+```python
+sewerrat.query(user="LTLA") # created by myself
+sewerrat.query(path="diet/") # path has 'diet/' in it
+
+import time
+sewerrat.query(after=time.time() - 3600) # created less than 1 hour ago
+```
+
+## Saving Bioconductor objects for registration
+
+We provide some convenience methods to quickly save Bioconductor objects and associated metadata for quick registration.
+For example, if we have the following objects:
+
+```python
+import biocframe
+df1 = biocframe.BiocFrame({ "X": [1,2,3,4,5] })
+df2 = biocframe.BiocFrame({ "Y": ["x", "y", "z"] })
+df3 = biocframe.BiocFrame({ "Z": [ 1.2, 3.4, 5.6, 7.8, 9.0 ] })
+```
+
+We use the `quickSave()` function to deposit them into a directory.
+(This uses the `r Biocpkg("alabaster.base")` package under the hood to create the on-disk representations.)
+
+```python
+biocdir = tempfile.mkdtemp()
+sewerrat.quick_save(df1, { "description": "This has integers" }, os.path.join(biocdir, "int"))
+sewerrat.quick_save(df2, { "description": "This has characters" }, os.path.join(biocdir, "char"))
+sewerrat.quick_save(df3, { "description": "This has reals" }, os.path.join(biocdir, "real"))
+```
+
+Then we can just register this directory with our SewerRat API.
+
+```python
+sewerrat.register(biocdir)
+```
+
+We can now query for these objects:
+
+```python
+res = sewerrat.query("integers")
+```
+
+And once we find something we like, we can load it back in quickly:
+
+```python
+x, meta = sewerrat.quick_read(res[0]["path"])
+```
+
+## Administrator instructions
+
+The URL to the SewerRat REST API depends on the instance and needs to be specified correctly before **sewerrat** functions can be used.
+Administrators of an R installation can achieve this by setting the `SEWERRAT_REST_URL` environment variable before **sewerrat** package load.
+Developers of packages that call **sewerrat** can either pass in a URL to the `url=` argument in various **sewerrat** functions,
+or they can globally set the URL via the `rest_url()` function.