Rename the project to "wellmap".

.bumpversion.cfg

@@ -5,5 +5,5 @@ tag = True
 
 [bumpversion:file:setup.py]
 
-[bumpversion:file:bio96/__init__.py]
+[bumpversion:file:wellmap/__init__.py]
 

.travis.yml

@@ -8,6 +8,6 @@ install:
     # paths in site-packages actually run.  I'm not totally sure.
     - pip install -e .
 script: 
-    - py.test tests --cov bio96
+    - py.test tests --cov wellmap
 after_success:
     - coveralls

README.rst

@@ -1,6 +1,6 @@
-*************************************************
-``bio96`` — File format for 96-well plate layouts
-*************************************************
+***************************************************
+``wellmap`` — File format for 96-well plate layouts
+***************************************************
 
 Many medium-throughput experiments produce data in 24-, 96-, or 384-well plate 
 format.  However, it can be a challenge to keep track of which wells (e.g. A1, 
@@ -10,32 +10,32 @@ can also be a challenge to write analysis scripts flexible enough to handle the
 different plate layouts that will inevitably come up as more and more 
 experiments are run.
 
-The ``bio96`` package solves these challenges by introducing a `TOML-based file 
+The ``wellmap`` package solves these challenges by introducing a `TOML-based file 
 format`__ that succinctly describes the organization of wells on plates.  The 
 file format is designed to be human-readable and -writable, so it can serve as 
 a standalone digital record.  The file format can also be easily parsed in 
 python and R to help write analysis scripts that will work regardless of how 
 you (or your collaborators) organize wells on your plates.
 
-__ https://bio96.readthedocs.io/en/latest/file_format.html
+__ https://wellmap.readthedocs.io/en/latest/file_format.html
 
-.. image:: https://img.shields.io/pypi/v/bio96.svg
-   :target: https://pypi.python.org/pypi/bio96
+.. image:: https://img.shields.io/pypi/v/wellmap.svg
+   :target: https://pypi.python.org/pypi/wellmap
 
-.. image:: https://img.shields.io/pypi/pyversions/bio96.svg
-   :target: https://pypi.python.org/pypi/bio96
+.. image:: https://img.shields.io/pypi/pyversions/wellmap.svg
+   :target: https://pypi.python.org/pypi/wellmap
 
-.. image:: https://img.shields.io/travis/kalekundert/bio96.svg
-   :target: https://travis-ci.org/kalekundert/bio96
+.. image:: https://img.shields.io/travis/kalekundert/wellmap.svg
+   :target: https://travis-ci.org/kalekundert/wellmap
 
-.. image:: https://readthedocs.org/projects/bio96/badge/?version=latest
-   :target: http://bio96.readthedocs.io/en/latest/
+.. image:: https://readthedocs.org/projects/wellmap/badge/?version=latest
+   :target: http://wellmap.readthedocs.io/en/latest/
 
-.. image:: https://img.shields.io/coveralls/kalekundert/bio96.svg
-   :target: https://coveralls.io/github/kalekundert/bio96?branch=master
+.. image:: https://img.shields.io/coveralls/kalekundert/wellmap.svg
+   :target: https://coveralls.io/github/kalekundert/wellmap?branch=master
 
 Documentation
 =============
-See the complete documentation `here <http://bio96.readthedocs.io/>`_.
+See the complete documentation `here <http://wellmap.readthedocs.io/>`_.
 
 .. image:: docs/example_layouts/qpcr_timecourse.svg

docs/_ext/example.py

@@ -35,13 +35,13 @@ def run(self):
     :caption: :download:`{name} </{toml_path}>`
 '''
         if 'no-figure' not in self.options:
-            import bio96
+            import wellmap
             import colorcet
 
-            df = bio96.load(toml_abs_path)
+            df = wellmap.load(toml_abs_path)
             attrs = self.options.get('attrs', [])
             cmap = colorcet.cm['rainbow']
-            fig = bio96.verify.plot_layout(df, attrs, cmap=cmap)
+            fig = wellmap.verify.plot_layout(df, attrs, cmap=cmap)
             fig.savefig(svg_abs_path, bbox_inches='tight')
 
             example_rst += f'''\
@@ -50,7 +50,7 @@ def run(self):
 '''
         example_str_list = StringList(example_rst.splitlines())
 
-        wrapper = nodes.container(classes=['bio96-example'])
+        wrapper = nodes.container(classes=['wellmap-example'])
         self.state.nested_parse(example_str_list, 0, wrapper)
         return [wrapper]
 

docs/_static/css/corrections.css

@@ -15,22 +15,22 @@
 
 /* Try to show the example code side-by-side with the image. */
 
-.rst-content .bio96-example {
+.rst-content .wellmap-example {
   display: flex;
   flex-flow: row wrap;
   align-items: center;
   margin: -4px;
   margin-bottom: 20px;
 }
 
-.rst-content .bio96-example div.figure {
+.rst-content .wellmap-example div.figure {
   margin: 4px;          /* This has a big bottom-margin by default.  That's now 
-                         * handled by the .bio96-example div.  The 4px margin 
+                         * handled by the .wellmap-example div.  The 4px margin 
                          * is needed to keep the flexbox spacing nice. */
   overflow-x: auto;
 }
 
-.rst-content .bio96-example div.literal-block-wrapper {
+.rst-content .wellmap-example div.literal-block-wrapper {
   margin: 4px;
   align-self: flex-start;
   flex: 1 0 50%;        /* Let the code grow, but don't let it take less than 
@@ -44,12 +44,12 @@
                          * big, I have to override this setting. */
 }
 
-.rst-content .bio96-example div.figure img {
+.rst-content .wellmap-example div.figure img {
   max-width: none;      /* Don't allow the images to shrink. */
 }
 
-.rst-content .bio96-example div[class^='highlight'] {
-  margin-bottom: 0px;   /* This margin is now handled by the .bio96-example 
+.rst-content .wellmap-example div[class^='highlight'] {
+  margin-bottom: 0px;   /* This margin is now handled by the .wellmap-example 
                          * div.*/
 }
 

docs/basic_usage.rst

@@ -2,17 +2,17 @@
 Basic usage
 ***********
 
-The following steps show how to get started with :mod:`bio96`:
+The following steps show how to get started with :mod:`wellmap`:
 
 .. make-list-from-sections::
 
-1. Install bio96
-================
-Install :mod:`bio96` from PyPI:
+1. Install wellmap
+==================
+Install :mod:`wellmap` from PyPI:
 
 .. code-block:: console
 
-  $ pip install bio96
+  $ pip install wellmap
 
 2. Describe the plate layout
 ============================
@@ -25,14 +25,14 @@ example, the following layout might be used for a standard curve:
 
 3. Confirm the plate layout
 ===========================
-Confirm that the layout is correct by using the :prog:`bio96` command-line 
+Confirm that the layout is correct by using the :prog:`wellmap` command-line 
 program to produce a visualization of the layout.  This is an important step, 
 because it's much easier to spot mistakes in the visualization than in the 
 layout file itself.
 
 .. code-block:: console
 
-   $ bio96 std_curve.toml
+   $ wellmap std_curve.toml
 
 This maps shows that:
 
@@ -53,7 +53,7 @@ the example standard curve layout.  This is qPCR data, where a higher
 
 5. Label the data
 =================
-Use `bio96.load()` to associate the labels specified in the TOML file (e.g. the 
+Use `wellmap.load()` to associate the labels specified in the TOML file (e.g. the 
 dilutions and replicates) with the experimental data (e.g. the :math:`C_q` 
 values).  This process has three steps:
 
@@ -63,11 +63,11 @@ values).  This process has three steps:
 
 For the sake of clarity and completeness, we will first show how to perform 
 these steps `manually <#manual-merge>`__.  Practically, though, it's easier to 
-let :mod:`bio96` perform them `automatically <#automatic-merge>`__.
+let :mod:`wellmap` perform them `automatically <#automatic-merge>`__.
 
 Manual merge
 ------------
-The first step is to use the `bio96.load()` function to create a 
+The first step is to use the `wellmap.load()` function to create a 
 `pandas.DataFrame` containing the information from the TOML file.  Note that 
 this data frame has columns for each label we specified: *replicate*, 
 *dilution*.  It also has six columns identifying the wells in different ways: 
@@ -80,9 +80,9 @@ can be used to calculate an appropriate merge column.
 
 .. code-block:: pycon
 
-   >>> import bio96
+   >>> import wellmap
    >>> import pandas as pd
-   >>> labels = bio96.load('std_curve.toml')
+   >>> labels = wellmap.load('std_curve.toml')
    >>> labels
       well well0 row col  row_i  col_j  replicate  dilution
    0    A1   A01   A   1      0      0          1  100000.0
@@ -167,11 +167,11 @@ names; see the documentation on :func:`pandas.merge` for more information.
 Automatic merge
 ---------------
 While it's good to understand how the labels are merged with the data, it's 
-better to let :mod:`bio96` perform the merge for you.  Not only is this 
+better to let :mod:`wellmap` perform the merge for you.  Not only is this 
 approach less code, it also handles some tricky corner cases behind the scenes, 
 e.g. layouts with multiple data files.  
 
-To load *and* merge the data using :func:`bio96.load`, you need to provide the 
+To load *and* merge the data using :func:`wellmap.load`, you need to provide the 
 following arguments:
 
 - **data_loader**: A function that accepts a path to a file and returns a 
@@ -193,7 +193,7 @@ unnecessary.
 
 .. code-block:: pycon
 
-   >>> df = bio96.load(
+   >>> df = wellmap.load(
    >>>         'std_curve.toml',
    >>>         data_loader=pd.read_csv,
    >>>         merge_cols=True,

docs/basic_usage/.ipynb_checkpoints/std_curve-checkpoint.ipynb

@@ -286,8 +286,8 @@
     }
    ],
    "source": [
-    "import bio96\n",
-    "labels = bio96.load('std_curve.toml')\n",
+    "import wellmap\n",
+    "labels = wellmap.load('std_curve.toml')\n",
     "labels"
    ]
   },

docs/basic_usage/std_curve.ipynb

@@ -286,8 +286,8 @@
     }
    ],
    "source": [
-    "import bio96\n",
-    "labels = bio96.load('std_curve.toml')\n",
+    "import wellmap\n",
+    "labels = wellmap.load('std_curve.toml')\n",
     "labels"
    ]
   },

docs/basic_usage/std_curve.py

@@ -1,9 +1,9 @@
 #!/usr/bin/env python3
 
-import bio96
+import wellmap
 
 import pandas as pd
-df = bio96.load(
+df = wellmap.load(
       'std_curve.toml',
       data_loader=pd.read_csv,
       merge_cols=True,

docs/command_line.rst

@@ -1,15 +1,15 @@
-.. prog:: bio96
+.. prog:: wellmap
 
 ******************
 Command-line usage
 ******************
-The :mod:`bio96` package comes with a command-line tool (also called 
-:prog:`bio96`) that displays a visual representation of the plate layout 
+The :mod:`wellmap` package comes with a command-line tool (also called 
+:prog:`wellmap`) that displays a visual representation of the plate layout 
 described by a TOML file.  This is meant to help catch mistakes, which can be 
 easy to make in complex layouts.
 
 For more information on this command and its options, run:
 
-.. command-output:: bio96 -h
+.. command-output:: wellmap -h
 
 

docs/conf.py

@@ -1,13 +1,13 @@
 import sys, os
-import bio96
+import wellmap
 sys.path.append(os.path.dirname(__file__))
 
 source_suffix = '.rst'
 master_doc = 'index'
-project = u'bio96'
+project = u'wellmap'
 copyright = u'2015, Kale Kundert'
-version = bio96.__version__
-release = bio96.__version__
+version = wellmap.__version__
+release = wellmap.__version__
 exclude_patterns = ['_build']
 templates_path = ['_templates']
 html_static_path = ['_static']

docs/example_layouts/beta_gal_assay.rst

@@ -13,6 +13,6 @@ depending on how much enzyme is expressed).  The *fit_start_min* and
 and should be used for the fit.  The default is to use the data points between 
 5–30 min, but it is easy to override this default on a per-well basis as 
 necessary.  This is an good example of how the fine-grained control provided by 
-:mod:`bio96` can be used to facilitate analysis.
+:mod:`wellmap` can be used to facilitate analysis.
 
 .. example:: beta_gal_assay.toml

docs/file_format.rst

@@ -2,7 +2,7 @@
 File format
 ***********
 
-The basic organization of a :mod:`bio96` file is as follows: first you specify 
+The basic organization of a :mod:`wellmap` file is as follows: first you specify 
 a group of wells, then you specify the experimental parameters associated with 
 those wells.  For example, the following snippet specifies that well A1 has a 
 concentration of 100:
@@ -45,7 +45,7 @@ parameter; missing values will be represented in the data frame by ``nan``.
 
 [meta]
 ======
-Miscellaneous fields that affect how :mod:`bio96` parses the file.  This is the 
+Miscellaneous fields that affect how :mod:`wellmap` parses the file.  This is the 
 only section that does not describe the organization of any wells.
 
 .. note::
@@ -195,7 +195,7 @@ Analysis scripts can still access this information using the **extras**
 argument to the `load()` function, but it will not clutter the data frame used 
 for analysis.
 
-Note that the :prog:`bio96` command by default only displays experimental 
+Note that the :prog:`wellmap` command by default only displays experimental 
 parameters that have at least two different values across the whole layout, 
 which normally excludes `[expt]` parameters.  To see these parameters anyways, 
 specify the ``<attr>`` argument.

docs/getting_help.rst

@@ -2,8 +2,8 @@
 Getting Help
 ************
 
-If you find a bug, or need help getting :mod:`bio96` to work, please open a new 
+If you find a bug, or need help getting :mod:`wellmap` to work, please open a new 
 issue_ on Github.  `Pull requests`_ are also welcome!
 
-.. _issue: https://github.com/kalekundert/bio96/issues
-.. _pull requests: https://github.com/kalekundert/bio96/pulls 
+.. _issue: https://github.com/kalekundert/wellmap/issues
+.. _pull requests: https://github.com/kalekundert/wellmap/pulls