Merge pull request #106 from alan-turing-institute/rename-source

Rename all references of PACE & pace to setvis
alan-turing-institute · Jan 29, 2023 · 949b310 · 949b310
2 parents b3f66b6 + 35d40e5
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diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # setvis [![Python Package](https://github.com/alan-turing-institute/setvis/actions/workflows/main.yml/badge.svg)](https://github.com/alan-turing-institute/setvis/actions/workflows/main.yml)
 
-A tool for visualising patterns of missingness in data. `setvis` is matrix-based set visualization that operates with datasets using a memory-efficient architecture.
+A tool for visualising patterns of missingness in data. Setvis is matrix-based set visualization that operates with datasets using a memory-efficient architecture.
 
 ## Installation
 
@@ -28,7 +28,8 @@ Then run either:
 ```
 pip install ".[extra]"
 ```
-which will install setvis (previously called PACE) and most of the optional extra dependencies
+
+which will install setvis and most of the optional extra dependencies
 
 or run:
 
@@ -58,10 +59,10 @@ The following dependencies place additional requirements on the environment wher
 
 #### Running the tutorial notebooks
 
-The Bokeh plots produced by PACE require the package `notebook >= 6.4` to display properly.
+The Bokeh plots produced by setvis require the package `notebook >= 6.4` to display properly.
 
 Installing the `notebook` extra dependency set (see above) will include everything
-required to run PACE in a notebook, and to run the tutorial examples
+required to run setvis in a notebook, and to run the tutorial examples
 that do not need a database connection. For the latter, install `db`
 as well.
 
@@ -92,7 +93,7 @@ cd setvis
 # Install the Bottleneck conda package and its dependencies
 conda install Bottleneck=1.3.2
 
-# Install pace itself and the remaining dependencies with pip
+# Install setvis itself and the remaining dependencies with pip
 pip install ".[all]"
 ```
 
@@ -118,4 +119,4 @@ poetry shell
 
 ## Acknowledgements
 
-The development of the PACE software was supported by funding from the Engineering and Physical Sciences Research Council (EP/N013980/1; EP/K503836/1) and the Alan Turing Institute.
+The development of the setvis software was supported by funding from the Engineering and Physical Sciences Research Council (EP/N013980/1; EP/K503836/1) and the Alan Turing Institute.
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -17,7 +17,7 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'PACE'
+project = 'setvis'
 copyright = '2021, pwochner, ots22, raruddle'
 author = 'pwochner, ots22, raruddle'
 

diff --git a/docs/source/history.rst b/docs/source/history.rst
@@ -1,7 +1,7 @@
 Selections and Selection History
 ================================
 
-.. automodule:: pace.history
+.. automodule:: setvis.history
    :members:
    :special-members: __getitem__, __setitem__
 
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -1,12 +1,12 @@
-.. PACE documentation master file, created by
+.. setvis documentation master file, created by
    sphinx-quickstart on Mon Nov 15 16:05:07 2021.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to PACE's documentation!
-================================
+Setvis Documentation Index
+==========================
 
-PACE is a python package for exploring and visualizing data
+Setvis is a python package for exploring and visualizing data
 missingness (that is, the presence, number and pattern of `missing
 data <https://en.wikipedia.org/wiki/Missing_data>`_ in a dataset).
 
@@ -16,10 +16,10 @@ missingness is a special case.
 It is designed to work particularly well when used interactively from
 a notebook, but can also be used non-interactively.
 
-At the moment, PACE can load data from `pandas
+At the moment, setvis can load data from `pandas
 <https://pandas.pydata.org/>`_ dataframes, csv files, and also
 supports a Postgres database backend.  It is designed with large
-datasets in mind -- PACE may be able to load the missingness
+datasets in mind -- setvis may be able to load the missingness
 information from a dataset even if the dataset itself does not fit
 in memory.
 
@@ -45,7 +45,7 @@ Put a couple of simple examples here
 Acknowledgements
 ================
 
-The development of the PACE software was supported by funding from the
+The development of the setvis software was supported by funding from the
 Engineering and Physical Sciences Research Council (EP/N013980/1;
 EP/K503836/1) and the Alan Turing Institute.
 

diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -1,4 +1,4 @@
-.. _installation-instructions: 
+.. _installation-instructions:
 
 Installation instructions
 =========================
@@ -8,14 +8,14 @@ Installation instructions
 Setting up the environment
 --------------------------
 
-PACE places relatively few requirements on the system environment it
+Setvis places relatively few requirements on the system environment it
 is installed in.  It is recommended to use a Python installation based
 on a virtual environment or Conda.  This could be as part of an
-existing project, or one set up specifically for running PACE by
+existing project, or one set up specifically for running setvis by
 following one of the configurations below.
 
 Once you are happy with your environmental set-up, continue to
-:ref:`installing-pace`.
+:ref:`installing-setvis`.
 
 
 Conda
@@ -42,7 +42,7 @@ This configuration has been tested with:
    conda install Bottleneck=1.3.2
 
 
-Next, :ref:`install PACE <installing-pace>`.
+Next, :ref:`install setvis <installing-setvis>`.
 
 
 Python venv (virtual environment)
@@ -54,11 +54,11 @@ This configuration has been tested with:
 
 .. code:: bash
 
-   # Create a virtual environment, in a new directory 'pace-venv'
-   python -m venv pace-venv
+   # Create a virtual environment, in a new directory 'setvis-venv'
+   python -m venv setvis-venv
 
    # Use the following command to activate the venv
-   source pace-venv/bin/activate
+   source setvis-venv/bin/activate
 
    # Upgrade pip once working inside
    pip install --upgrade pip
@@ -67,13 +67,13 @@ This configuration has been tested with:
 - `Python documentation on virtual environments <https://docs.python.org/3/tutorial/venv.html>`_
 
 
-Next, :ref:`install PACE <installing-pace>`.
+Next, :ref:`install setvis <installing-setvis>`.
 
 
-.. _installing-pace:
+.. _installing-setvis:
 
-Installing PACE
----------------
+Installing setvis
+-----------------
 
 Once your environment is set up and activated, and follow one of the
 sets of instructions below.
@@ -104,7 +104,7 @@ Most users should then run
 
    pip install ".[extra]"
 
-which will install PACE and most of the optional extra dependencies.
+which will install setvis and most of the optional extra dependencies.
 
 
 Alternatively, run
@@ -113,13 +113,13 @@ Alternatively, run
 
    pip install .
 
-which will include PACE and a minimal set of dependencies.
+which will include setvis and a minimal set of dependencies.
 
 The part of the package in square brackets above ('[extra]') is a pip
 `dependency extra <https://peps.python.org/pep-0508/#extras>`_ for
 selecting optional extra packages to install. See the :ref:`next
 section <package-extras>` for a full list of these options, which can
-be used to configure the PACE installation.
+be used to configure the setvis installation.
 
 
 .. _package-extras:
@@ -128,7 +128,7 @@ Extras and fine-tuning the installation
 .......................................
 
 This section applies whatever the source of the installation (from
-PyPI or GitHub).  PACE supports several optional features that can be
+PyPI or GitHub).  Setvis supports several optional features that can be
 installed by passing various extra dependency flags to pip.
 
 For instance: ``pip install ".[notebook]"`` (which installs the
@@ -159,13 +159,13 @@ environment where the package is to be installed:
 
 
 
-Installing PACE with Poetry (developers)
+Installing setvis with Poetry (developers)
 ----------------------------------------
 
 This project uses `Poetry <https://python-poetry.org/>`_ for
-dependency management and packaging.  To contribute to PACE
+dependency management and packaging.  To contribute to setvis
 development, follow the instructions below to set up a virtual
-environment containing PACE and its dependencies.  See the `poetry
+environment containing setvis and its dependencies.  See the `poetry
 documentation <https://python-poetry.org/docs/>`_ for how to use this
 for dependency management.
 

diff --git a/docs/source/membership.rst b/docs/source/membership.rst
@@ -1,5 +1,5 @@
-PACE fundamentals and the Membership class
+Setvis fundamentals and the Membership class
 ==========================================
 
-.. automodule:: pace.membership
+.. automodule:: setvis.membership
    :members:
diff --git a/docs/source/plots.rst b/docs/source/plots.rst
@@ -1,6 +1,6 @@
 Plotting and interactivity
 ==========================
 
-.. automodule:: pace.plots
+.. automodule:: setvis.plots
    :members:
 
diff --git a/docs/source/set_expression.rst b/docs/source/set_expression.rst
@@ -1,7 +1,7 @@
 Set Expressions
 ===============
 
-.. automodule:: pace.setexpression
+.. automodule:: setvis.setexpression
    :members:
    :show-inheritance:
    :member-order: bysource
diff --git a/docs/source/tutorials.rst b/docs/source/tutorials.rst
@@ -1,13 +1,13 @@
 Tutorials
 =========
 
-The PACE repository includes some tutorials and extended examples in
+The setvis repository includes some tutorials and extended examples in
 the form of Jupyter notebooks.  The tutorials are designed to
-introduce PACE concepts and be run interactively.
+introduce setvis concepts and be run interactively.
 
 This section describes how to install and run these.
 
-The source for all notebooks can be found `within the PACE GitHub
+The source for all notebooks can be found `within the setvis GitHub
 repository
 <https://github.com/alan-turing-institute/visualising-data-profiles/tree/main/notebooks>`_.
 
@@ -17,7 +17,7 @@ Install and run the notebooks
 
 To access the tutorials, after setting up a suitable python
 environment (see the :ref:`relevant section of the installation
-instructions <python-env-setup>`), clone and install PACE from GitHub
+instructions <python-env-setup>`), clone and install setvis from GitHub
 source.
 
 .. code:: bash
@@ -28,7 +28,7 @@ source.
 
 
 Then run the command below to install the ``notebook`` extra dependency
-set, which will include everything required to run PACE in a notebook,
+set, which will include everything required to run setvis in a notebook,
 and to run the tutorial examples that do not need a database
 connection.
 
@@ -52,8 +52,8 @@ notebooks in the ``notebooks`` directory of the repository:
 
 .. warning::
 
-   The Bokeh plots produced by PACE require the package ``notebook``
-   with version **>= 6.4** in order to display properly.  If PACE is
+   The Bokeh plots produced by setvis require the package ``notebook``
+   with version **>= 6.4** in order to display properly.  If setvis is
    installed as described above, this will be included automatically.
-   If using a 'minimal' PACE installation alongside an existing
+   If using a 'minimal' setvis installation alongside an existing
    notebook installation, please ensure that this requirement is met.
diff --git a/notebooks/Example - import data to visualize missingness.ipynb b/notebooks/Example - import data to visualize missingness.ipynb
@@ -33,8 +33,8 @@
    "source": [
     "import pandas as pd\n",
     "\n",
-    "from pace import Membership\n",
-    "from pace.plots import PlotSession"
+    "from setvis import Membership\n",
+    "from setvis.plots import PlotSession"
    ]
   },
   {

diff --git a/notebooks/Example - import data to visualize sets.ipynb b/notebooks/Example - import data to visualize sets.ipynb
@@ -33,8 +33,8 @@
    "source": [
     "import pandas as pd\n",
     "\n",
-    "from pace import Membership\n",
-    "from pace.plots import PlotSession"
+    "from setvis import Membership\n",
+    "from setvis.plots import PlotSession"
    ]
   },
   {

diff --git a/notebooks/Example - plot outside notebook.ipynb b/notebooks/Example - plot outside notebook.ipynb
@@ -7,7 +7,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from pace.plots import *"
+    "from setvis.plots import *"
    ]
   },
   {

diff --git a/notebooks/Membership.ipynb b/notebooks/Membership.ipynb
@@ -17,7 +17,7 @@
    "source": [
     "import pandas as pd\n",
     "import numpy as np\n",
-    "from pace import Membership, Col"
+    "from setvis import Membership, Col"
    ]
   },
   {

diff --git a/notebooks/Performance.ipynb b/notebooks/Performance.ipynb
@@ -17,8 +17,8 @@
    "source": [
     "import pandas as pd\n",
     "import numpy as np\n",
-    "from pace.membership import Membership, Col, set_bar_chart_data\n",
-    "from pace.setexpression import Set"
+    "from setvis.membership import Membership, Col, set_bar_chart_data\n",
+    "from setvis.setexpression import Set"
    ]
   },
   {

diff --git a/notebooks/Postgres example.ipynb b/notebooks/Postgres example.ipynb
@@ -7,7 +7,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from pace.membership import *\n",
+    "from setvis.membership import *\n",
     "\n",
     "import psycopg2\n",
     "from psycopg2.extensions import connection\n",

diff --git a/notebooks/Set Mode Example.ipynb b/notebooks/Set Mode Example.ipynb
@@ -10,8 +10,8 @@
     "import pandas as pd\n",
     "from pathlib import Path\n",
     "\n",
-    "from pace import Membership\n",
-    "from pace.plots import PlotSession"
+    "from setvis import Membership\n",
+    "from setvis.plots import PlotSession"
    ]
   },
   {