Merge pull request #219 from Roche/dev

version 1.2.1

Author: ofajardo

CITATION.cff

@@ -5,7 +5,7 @@ authors:
   given-names: "Otto"
   orcid: "https://orcid.org/0000-0002-3363-9287"
 title: "Pyreadstat"
-version: 1.2.0
+version: 1.2.1
 doi: 10.5281/zenodo.6612282
 date-released: 2018-09-24
 url: "https://github.com/Roche/pyreadstat"

README.md

@@ -45,6 +45,7 @@ the original applications in this regard.**
     - [Missing Values](#missing-values)
       + [SPSS](#spss)
       + [SAS and STATA](#sas-and-stata)
+    - [Reading datetime and date columns](#reading-datetime-and-date-columns)
     - [Other options](#other-options)
   + [More writing options](#more-writing-options)
     - [File specific options](#file-specific-options)
@@ -637,6 +638,36 @@ This is a list listing all user defined missing values.
 User defined missing values are currently not supported for file types other than sas7bdat,
 sas7bcat and dta.
 
+#### Reading datetime and date columns
+
+SAS, SPSS and STATA represent datetime, date and other similar concepts as a numeric column and then applies a 
+display format on top. Roughly speaking, internally there are two possible representations: one for concepts with a day or lower 
+granularity (date, week, quarter, year, etc.) and those with a higher granularity than a day (datetime, time, hour, etc).
+The first group is suceptible to be converted to a python date object and the second to a python datetime object. 
+
+Pyreadstat attempts to read columns with datetime, date and time formats that are convertible
+to python datetime, date and time objects automatically. However there are other formats that are not fully convertible to
+any of these formats, for example SAS "YEAR" (displaying only the year), "MMYY" (displaying only month and year), etc.
+Because there are too many of these formats and these keep changing, it is not possible to implement a rule for each of
+those, therefore these columns are not transformed and the user will obtain a numeric column. 
+
+In order to cope with this issue, there are two options for each reader function: extra\_datetime\_formats and
+ extra\_date\_formats that allow the user to
+pass these datetime or date formats, to transform the numeric values into datetime or date python objects. Then, the user
+can format those columns appropiately; for example extracting the year only to an integer column in the case of 'YEAR' or
+formatting it to a string 'YYYY-MM' in the case of 'MMYY'. The choice between datetime or date format depends on the granularity
+of the data as explained above.
+
+This arguments are also useful in the case you have a valid datetime, date or time format that is currently not recognized in pyreadstat.
+In those cases, feel free to file an issue to ask those to be added to the list, in the meantime you can use these arguments to do
+the conversion.
+
+```python
+import pyreadstat
+
+df, meta = pyreadstat.read_sas7bdat('/path/to/a/file.sas7bdat', extra_date_formats=["YEAR", "MMYY"])
+```
+
 #### Other options
 
 You can set the encoding of the original file manually. The encoding must be a [iconv-compatible encoding](https://gist.github.com/hakre/4188459).

change_log.md

@@ -1,3 +1,11 @@
+# 1.2.1 (github, pypi and conda 2023.02.22)
+* Readstat source updated to version 1.1.9
+* introduced recognition for pandas datatype datetime64[ns, UTC] and other datetime64 types when writing, 
+  so that this column type gets correctly written as datetime
+* introduced extra_datetime_formats and extra_date_formats arguments for read functions, cleaned the list of 
+  sas date, datetime and time formats to exclude those not directly convertible to python objects
+* improved performace of writer when there are datetime64 columns
+
 # 1.2.0 (github, pypi and conda 2022.10.25)
 * Fixed #206, #207
 * added pyproject.toml

docs/_build/doctrees/environment.pickle

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: d1957ba96adbb9536e51c852822e9ccb
+config: dc63e4405a0437fb9efe8c4f5ffb3848
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_build/doctrees/index.doctree

@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '1.2.0',
+    VERSION: '1.2.1',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

docs/_build/html/.buildinfo

@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Index &mdash; pyreadstat 1.2.0 documentation</title>
+  <title>Index &mdash; pyreadstat 1.2.1 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>

docs/_build/html/_static/documentation_options.js

@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Welcome to pyreadstat’s documentation! &mdash; pyreadstat 1.2.0 documentation</title>
+  <title>Welcome to pyreadstat’s documentation! &mdash; pyreadstat 1.2.1 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>
@@ -154,6 +154,8 @@ <h1>Metadata Object Description<a class="headerlink" href="#metadata-object-desc
 <li><p><strong>output_format</strong> (<em>str</em><em>, </em><em>optional</em>) – one of ‘pandas’ (default) or ‘dict’. If ‘dict’ a dictionary with numpy arrays as values will be returned, the
 user can then convert it to her preferred data format. Using dict is faster as the other types as the conversion to a pandas
 dataframe is avoided.</p></li>
+<li><p><strong>extra_datetime_formats</strong> (<em>list of str</em><em>, </em><em>optional</em>) – formats to be parsed as python datetime objects</p></li>
+<li><p><strong>extra_date_formats</strong> (<em>list of str</em><em>, </em><em>optional</em>) – formats to be parsed as python date objects</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns</dt>
@@ -252,6 +254,8 @@ <h1>Metadata Object Description<a class="headerlink" href="#metadata-object-desc
 <li><p><strong>output_format</strong> (<em>str</em><em>, </em><em>optional</em>) – one of ‘pandas’ (default) or ‘dict’. If ‘dict’ a dictionary with numpy arrays as values will be returned, the
 user can then convert it to her preferred data format. Using dict is faster as the other types as the conversion to a pandas
 dataframe is avoided.</p></li>
+<li><p><strong>extra_datetime_formats</strong> (<em>list of str</em><em>, </em><em>optional</em>) – formats to be parsed as python datetime objects</p></li>
+<li><p><strong>extra_date_formats</strong> (<em>list of str</em><em>, </em><em>optional</em>) – formats to be parsed as python date objects</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns</dt>
@@ -335,6 +339,8 @@ <h1>Metadata Object Description<a class="headerlink" href="#metadata-object-desc
 <li><p><strong>output_format</strong> (<em>str</em><em>, </em><em>optional</em>) – one of ‘pandas’ (default) or ‘dict’. If ‘dict’ a dictionary with numpy arrays as values will be returned, the
 user can then convert it to her preferred data format. Using dict is faster as the other types as the conversion to a pandas
 dataframe is avoided.</p></li>
+<li><p><strong>extra_datetime_formats</strong> (<em>list of str</em><em>, </em><em>optional</em>) – formats to be parsed as python datetime objects</p></li>
+<li><p><strong>extra_date_formats</strong> (<em>list of str</em><em>, </em><em>optional</em>) – formats to be parsed as python date objects</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns</dt>
@@ -384,6 +390,8 @@ <h1>Metadata Object Description<a class="headerlink" href="#metadata-object-desc
 <li><p><strong>output_format</strong> (<em>str</em><em>, </em><em>optional</em>) – one of ‘pandas’ (default) or ‘dict’. If ‘dict’ a dictionary with numpy arrays as values will be returned, the
 user can then convert it to her preferred data format. Using dict is faster as the other types as the conversion to a pandas
 dataframe is avoided.</p></li>
+<li><p><strong>extra_datetime_formats</strong> (<em>list of str</em><em>, </em><em>optional</em>) – formats to be parsed as python datetime objects</p></li>
+<li><p><strong>extra_date_formats</strong> (<em>list of str</em><em>, </em><em>optional</em>) – formats to be parsed as python date objects</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns</dt>
@@ -422,6 +430,8 @@ <h1>Metadata Object Description<a class="headerlink" href="#metadata-object-desc
 <li><p><strong>output_format</strong> (<em>str</em><em>, </em><em>optional</em>) – one of ‘pandas’ (default) or ‘dict’. If ‘dict’ a dictionary with numpy arrays as values will be returned, the
 user can then convert it to her preferred data format. Using dict is faster as the other types as the conversion to a pandas
 dataframe is avoided.</p></li>
+<li><p><strong>extra_datetime_formats</strong> (<em>list of str</em><em>, </em><em>optional</em>) – formats to be parsed as python datetime objects</p></li>
+<li><p><strong>extra_date_formats</strong> (<em>list of str</em><em>, </em><em>optional</em>) – formats to be parsed as python date objects</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns</dt>

docs/_build/html/genindex.html

@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Python Module Index &mdash; pyreadstat 1.2.0 documentation</title>
+  <title>Python Module Index &mdash; pyreadstat 1.2.1 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>

docs/_build/html/index.html

@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Search &mdash; pyreadstat 1.2.0 documentation</title>
+  <title>Search &mdash; pyreadstat 1.2.1 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
 

docs/_build/html/py-modindex.html

@@ -26,7 +26,7 @@
 # The short X.Y version
 version = ''
 # The full version, including alpha/beta/rc tags
-release = '1.2.0'
+release = '1.2.1'
 
 
 # -- General configuration ---------------------------------------------------