From a5f26a1c7878e8afa0714aa8be502cb7bbad0516 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Therese=20Natter=C3=B8y?=
 <61694854+tnatt@users.noreply.github.com>
Date: Mon, 15 Apr 2024 14:19:17 +0200
Subject: [PATCH] =?UTF-8?q?=C2=A0CLN:=20Deprecate=20table=5Finclude=5Finde?=
 =?UTF-8?q?x?=
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---
 src/fmu/dataio/_utils.py |  6 +++++-
 src/fmu/dataio/dataio.py | 38 +++++++++++++++-----------------------
 2 files changed, 20 insertions(+), 24 deletions(-)

diff --git a/src/fmu/dataio/_utils.py b/src/fmu/dataio/_utils.py
index 6cda44d93..d26d6c0ff 100644
--- a/src/fmu/dataio/_utils.py
+++ b/src/fmu/dataio/_utils.py
@@ -140,7 +140,11 @@ def export_file(
     ):
         obj.to_file(filename, fformat="roff")
     elif filename.suffix == ".csv" and isinstance(obj, pd.DataFrame):
-        obj.to_csv(filename, index=flag == "include_index")
+        logger.info(
+            "Exporting dataframe to csv. Note: index columns will not be "
+            "preserved unless calling 'reset_index()' on the dataframe."
+        )
+        obj.to_csv(filename, index=False)
     elif filename.suffix == ".arrow":
         from pyarrow import Table
 
diff --git a/src/fmu/dataio/dataio.py b/src/fmu/dataio/dataio.py
index 48b6555ee..61909cbbd 100644
--- a/src/fmu/dataio/dataio.py
+++ b/src/fmu/dataio/dataio.py
@@ -13,7 +13,6 @@
 from typing import Any, ClassVar, Final, List, Literal, Optional, Union
 from warnings import warn
 
-import pandas as pd
 from pydantic import ValidationError as PydanticValidationError
 
 from . import types
@@ -26,7 +25,7 @@
 from ._utils import (
     create_symlink,
     detect_inside_rms,  # dataio_examples,
-    export_file_compute_checksum_md5,
+    export_file,
     export_metadata_file,
     prettyprint_dict,
     read_metadata_from_file,
@@ -299,9 +298,8 @@ class ExportData:
 
         grid_model: Currently allowed but planned for deprecation
 
-        include_index: This applies to Pandas (table) data only, and if True then the
-            index column will be exported. Deprecated, use class variable
-            ``table_include_index`` instead
+        table_index: This applies to Pandas (table) data only, and is a list of the
+            column names to use as index columns e.g. ["ZONE", "REGION"].
 
         is_prediction: True (default) if model prediction data
 
@@ -399,7 +397,7 @@ class ExportData:
     surface_fformat: ClassVar[str] = "irap_binary"
     table_fformat: ClassVar[str] = "csv"
     dict_fformat: ClassVar[str] = "json"
-    table_include_index: ClassVar[bool] = False
+    table_include_index: ClassVar[bool] = False  # deprecated
     verifyfolder: ClassVar[bool] = True  # deprecated
     _inside_rms: ClassVar[bool] = False  # developer only! if True pretend inside RMS
 
@@ -529,6 +527,13 @@ def _show_deprecations_or_notimplemented(self) -> None:
                 "Please remove it from the argument list.",
                 UserWarning,
             )
+        if self.table_include_index:
+            warn(
+                "The 'table_include_index' option is deprecated and has no effect. "
+                "To get the index included in your dataframe, reset the index "
+                "before exporting the dataframe with dataio i.e. df = df.reset_index()",
+                UserWarning,
+            )
         if self.verbosity != "DEPRECATED":
             warn(
                 "Using the 'verbosity' key is now deprecated and will have no "
@@ -814,8 +819,7 @@ def export(
         Returns:
             String: full path to exported item.
         """
-        self.table_index = kwargs.get("table_index", self.table_index)
-        self.generate_metadata(obj, compute_md5=False, **kwargs)
+        self.generate_metadata(obj, compute_md5=True, **kwargs)
         metadata = self._metadata
         logger.info("Object type is: %s", type(self._object))  # from generate_metadata
 
@@ -824,21 +828,9 @@ def export(
         outfile.parent.mkdir(parents=True, exist_ok=True)
         metafile = outfile.parent / ("." + str(outfile.name) + ".yml")
 
-        useflag = (
-            self.table_include_index
-            if isinstance(self._object, pd.DataFrame)
-            else self._usefmtflag
-        )
-
-        logger.info("Export to file and compute MD5 sum, using flag: <%s>", useflag)
-
-        # inject md5 checksum in metadata
-        metadata["file"]["checksum_md5"] = export_file_compute_checksum_md5(
-            self._object,
-            outfile,
-            flag=useflag,  # type: ignore
-            # BUG(?): Looks buggy, if flag is bool export_file will blow up.
-        )
+        logger.info("Export to file using flag: <%s>", self._usefmtflag)
+        # md5sum is already present in the metadata
+        export_file(self._object, outfile, flag=self._usefmtflag)
         logger.info("Actual file is:   %s", outfile)
 
         if self._config_is_valid: