Merge pull request #5 from Krande/dev

Major improvement on handling Table formatting and numbering on docx export

.github/workflows/ci.yml

@@ -55,15 +55,13 @@ jobs:
           activate-environment: anaconda-client-env
           python-version: ${{ matrix.pyver.distver }}
           environment-file: conda/environment.yml
-
       - name: build, test and upload conda package
         if: github.event_name == 'push' && github.ref == 'refs/heads/main'
         env:
           ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
         shell: bash -l {0}
         run: |
           conda-build -c krande -c conda-forge conda --python=${{ matrix.pyver.distver }} --token=$ANACONDA_TOKEN --user krande --override-channels
-
       - name: build and test conda package
         if: github.event_name == 'push' && github.ref != 'refs/heads/main'
         shell: bash -l {0}

conda/environment.yml

@@ -1,5 +1,6 @@
 name: anaconda-client-env
 channels:
+  - krande
   - conda-forge
 dependencies:
   - conda-build

files/doc_math/00-main/00-intro.md

@@ -1,8 +1,8 @@
 # A List of functions
 
-Here are two basic function @eq:my_equation and @eq:my_equation_2.
+Here are two basic function @eq:my_equation_1 and @eq:my_equation_2.
 
-{{__my_equation__}}
+{{__my_equation_1__}}
 
 
 And here is a small edit of that function

files/doc_math/metadata.yaml

@@ -1,5 +1,7 @@
 lang: en-GB
+date: \today
+urlcolor: "black"
 linkReferences: true
 nameInLink: true
 figPrefix: "Figure"
-tblPrefix: "Table"
+tblPrefix: "Table"

files/doc_table/00-main/table.md

@@ -4,4 +4,6 @@ Some text before the table
 
 {{__my_table__}}
 
+{{__my_table_3__}}
+
 And some text after

files/doc_table/01-app/table.md

@@ -4,4 +4,8 @@ Some text before the table
 
 {{__my_table_2__}}
 
+{{__my_table_4__}}
+
+{{__my_table_5__}}
+
 and some text after

setup.py

@@ -1,3 +1,3 @@
 from setuptools import setup
 
-setup(version="0.0.3")
+setup(version="0.0.4")

src/paradoc/common.py

@@ -1,8 +1,9 @@
 from __future__ import annotations
 
 import pathlib
-from dataclasses import dataclass
-from typing import Callable
+import re
+from dataclasses import dataclass, field
+from typing import Callable, List, Union
 
 import pandas as pd
 
@@ -15,6 +16,7 @@ class TableFormat:
     style: str = "Grid Table 1 Light"
     font_size: float = 11
     font_style: str = "Arial"
+    float_fmt: Union[str, tuple] = None
 
 
 class TableFlags:
@@ -27,19 +29,29 @@ class Table:
     df: pd.DataFrame
     caption: str
     format: TableFormat = TableFormat()
-    add_link: bool = False
+    add_link: bool = True
+    md_instances: List[MarkDownFile] = field(default_factory=list)
+    docx_instances: List[object] = field(default_factory=list)
+
+    # def get_cell0(self):
+    #     col_name = self.df.columns[0]
+    #     df.iloc[0, df.columns.get_loc(col_name)]
 
     def to_markdown(self, include_name_in_cell=False, flags=None):
         df = self.df.copy()
         if include_name_in_cell:
             col_name = df.columns[0]
             df.iloc[0, df.columns.get_loc(col_name)] = self.name
-        tbl_str = df.to_markdown(index=False, tablefmt="grid")
+
+        props = dict(index=False, tablefmt="grid")
+        if self.format.float_fmt is not None:
+            props["floatfmt"] = self.format.float_fmt
+        tbl_str = df.to_markdown(**props)
         if flags is not None and TableFlags.NO_CAPTION in flags:
             return tbl_str
         tbl_str += f"\n\nTable: {self.caption}"
         if self.add_link:
-            tbl_str += f"{{#tbl:{self.name}}}"
+            tbl_str += f" {{#tbl:{self.name}}}"
         return tbl_str
 
 
@@ -48,12 +60,16 @@ class Equation:
     name: str
     func: Callable
     custom_eq_str_compiler: Callable = None
+    add_link: bool = True
+    include_python_code: bool = False
+    md_instances: List[MarkDownFile] = field(default_factory=list)
+    docx_instances: List[object] = field(default_factory=list)
 
     def to_latex(self, print_latex=False, print_formula=False, flags=None):
         if self.custom_eq_str_compiler is not None:
             return self.custom_eq_str_compiler(self.func)
 
-        from inspect import getsourcelines
+        from inspect import getsource, getsourcelines
 
         import pytexit
 
@@ -68,8 +84,14 @@ def to_latex(self, print_latex=False, print_formula=False, flags=None):
                 continue
             if dots >= 6 or dots == 0:
                 eq_latex += pytexit.py2tex(line, print_latex=print_latex, print_formula=print_formula) + "\n"
+        eq_str = eq_latex
+
+        if self.add_link:
+            eq_str += f"{{#eq:{self.name}}}"
 
-        return eq_latex + f"{{#eq:{self.name}}}"
+        if self.include_python_code:
+            eq_str = f"\n\n```python\n{getsource(self.func)}\n```\n\n" + eq_str
+        return eq_str
 
 
 @dataclass
@@ -85,6 +107,20 @@ class MarkDownFile:
     new_file: pathlib.Path
     build_file: pathlib.Path
 
+    def read_original_file(self):
+        with open(self.path, "r") as f:
+            return f.read()
+
+    def read_built_file(self):
+        """Read the Markdown file after performed variable substitution"""
+        with open(self.build_file, "r") as f:
+            return f.read()
+
+    def get_variables(self):
+        md_doc_str = self.read_original_file()
+        key_re = re.compile("{{(.*)}}")
+        return key_re.finditer(md_doc_str)
+
 
 class ExportFormats:
     DOCX = "docx"

src/paradoc/document.py

@@ -7,7 +7,6 @@
 from typing import Dict
 
 import pandas as pd
-import pypandoc
 
 from .common import (
     DocXFormat,
@@ -17,7 +16,8 @@
     Table,
     TableFormat,
 )
-from .utils import get_list_of_files, variable_sub
+from .exceptions import LatexNotInstalled
+from .utils import get_list_of_files
 
 
 class OneDoc:
@@ -49,11 +49,11 @@ class OneDoc:
         "Body Text": "Normal Indent",
         "Compact": "Normal Indent",
     }
+    FORMATS = ExportFormats
 
     def __init__(
         self,
         source_dir=None,
-        export_format=ExportFormats.DOCX,
         main_prefix="00-main",
         app_prefix="01-app",
         clean_build_dir=True,
@@ -64,7 +64,6 @@ def __init__(
         self.work_dir = kwargs.get("work_dir", pathlib.Path("").resolve().absolute())
         self._main_prefix = main_prefix
         self._app_prefix = app_prefix
-        self.export_format = export_format
         self.variables = dict()
         self.tables: Dict[str, Table] = dict()
         self.equations: Dict[str, Equation] = dict()
@@ -73,9 +72,9 @@ def __init__(
         # Style info: https://python-docx.readthedocs.io/en/latest/user/styles-using.html
         self.paragraph_style_map = kwargs.get("paragraph_style_map", OneDoc.default_paragraph_map)
         self.appendix_heading_map = kwargs.get("appendix_heading_map", OneDoc.default_app_map)
-
         self.md_files_main = []
         self.md_files_app = []
+        self.metadata_file = None
 
         for md_file in get_list_of_files(self.source_dir, ".md"):
             is_appendix = True if app_prefix in md_file else False
@@ -101,65 +100,106 @@ def __init__(
         if clean_build_dir is True:
             shutil.rmtree(self.build_dir, ignore_errors=True)
 
-    def compile(self, output_name, auto_open=False, metadata_file=None):
-        dest_file = (self.dist_dir / output_name).with_suffix(f".{self.export_format}").resolve().absolute()
+    def compile(self, output_name, auto_open=False, metadata_file=None, export_format=ExportFormats.DOCX, **kwargs):
+        dest_file = (self.dist_dir / output_name).with_suffix(f".{export_format}").resolve().absolute()
 
         logging.debug(f'Compiling report to "{dest_file}"')
         os.makedirs(self.build_dir, exist_ok=True)
         os.makedirs(self.dist_dir, exist_ok=True)
 
-        for mdf in self.md_files_main + self.md_files_app:
-            md_file = mdf.path
-            os.makedirs(mdf.new_file.parent, exist_ok=True)
+        self.metadata_file = self.source_dir / "metadata.yaml" if metadata_file is None else pathlib.Path(metadata_file)
 
-            # Substitute parameters/tables in the creation of the document
-            with open(md_file, "r") as f:
-                tmp_md_doc = f.read()
-                tmp_md_doc = variable_sub(tmp_md_doc, self.tables)
-                tmp_md_doc = variable_sub(tmp_md_doc, self.variables)
-                tmp_md_doc = variable_sub(tmp_md_doc, self.equations)
+        if self.metadata_file.exists() is False:
+            with open(self.metadata_file, "w") as f:
+                f.write('linkReferences: true\nnameInLink: true\nfigPrefix: "Figure"\ntblPrefix: "Table"')
 
-            with open(mdf.build_file, "w") as f:
-                f.write(tmp_md_doc)
-
-            metadata_file = self.source_dir / "metadata.yaml" if metadata_file is None else metadata_file
-            if metadata_file.exists() is False:
-                with open(metadata_file, "w") as f:
-                    f.write('linkReferences: true\nnameInLink: true\nfigPrefix: "Figure"\ntblPrefix: "Table"')
-
-            pypandoc.convert_file(
-                str(mdf.build_file),
-                self.export_format,
-                outputfile=str(mdf.new_file),
-                format="markdown",
-                extra_args=[
-                    "-M2GB",
-                    "+RTS",
-                    "-K64m",
-                    "-RTS",
-                    f"--resource-path={md_file.parent}",
-                    f"--metadata-file={metadata_file}"
-                    # f"--reference-doc={MY_DOCX_TMPL}",
-                ],
-                filters=["pandoc-crossref"],
-                encoding="utf8",
-            )
-        if self.export_format == ExportFormats.DOCX:
+        if export_format == ExportFormats.DOCX:
             from paradoc.io.word.exporter import WordExporter
 
-            wordx = WordExporter(self)
-            wordx.convert_to_docx(output_name, dest_file)
+            use_custom_compile = kwargs.get("use_custom_docx_compile", True)
+            if use_custom_compile is False:
+                use_table_name_in_cell_as_index = False
+            else:
+                use_table_name_in_cell_as_index = True
+
+            self._perform_variable_substitution(use_table_name_in_cell_as_index)
+
+            wordx = WordExporter(self, **kwargs)
+            wordx.export(output_name, dest_file)
+        elif export_format == ExportFormats.PDF:
+            from paradoc.io.pdf.exporter import PdfExporter
+
+            latex_path = shutil.which("latex")
+            if latex_path is None:
+                latex_url = "https://www.latex-project.org/get/"
+                raise LatexNotInstalled(
+                    "Latex was not installed on your system. "
+                    f'Please install latex before exporting to pdf. See "{latex_url}" for installation packages'
+                )
+            self._perform_variable_substitution(False)
+            pdf = PdfExporter(self)
+            pdf.export(dest_file)
+        else:
+            raise NotImplementedError(f'Export format "{export_format}" is not yet supported')
 
         if auto_open is True:
             os.startfile(dest_file)
 
-    def add_table(self, name, df: pd.DataFrame, caption: str, tbl_format: TableFormat = TableFormat()):
+    def add_table(self, name, df: pd.DataFrame, caption: str, tbl_format: TableFormat = TableFormat(), **kwargs):
         if '"' in caption:
             raise ValueError('Using characters such as " currently breaks the caption search in the docs compiler')
-        self.tables[name] = Table(name, df, caption, tbl_format)
+        self._uniqueness_check(name)
+        self.tables[name] = Table(name, df, caption, tbl_format, **kwargs)
 
-    def add_equation(self, name, eq, custom_eq_str_compiler=None):
-        self.equations[name] = Equation(name, eq, custom_eq_str_compiler=custom_eq_str_compiler)
+    def add_equation(self, name, eq, custom_eq_str_compiler=None, **kwargs):
+        self._uniqueness_check(name)
+        self.equations[name] = Equation(name, eq, custom_eq_str_compiler=custom_eq_str_compiler, **kwargs)
+
+    def _perform_variable_substitution(self, use_table_var_substitution):
+        logging.info("Performing variable substitution")
+        for mdf in self.md_files_main + self.md_files_app:
+            md_file = mdf.path
+            os.makedirs(mdf.new_file.parent, exist_ok=True)
+            md_str = mdf.read_original_file()
+            for m in mdf.get_variables():
+                res = m.group(1)
+                key = res.split("|")[0] if "|" in res else res
+                list_of_flags = res.split("|")[1:] if "|" in res else None
+                key_clean = key[2:-2]
+
+                tbl = self.tables.get(key_clean, None)
+                eq = self.equations.get(key_clean, None)
+                variables = self.variables.get(key_clean, None)
+
+                if tbl is not None:
+                    tbl.md_instances.append(mdf)
+                    new_str = tbl.to_markdown(use_table_var_substitution, list_of_flags)
+                elif eq is not None:
+                    eq.md_instances.append(mdf)
+                    new_str = eq.to_latex()
+                elif variables is not None:
+                    new_str = str(variables)
+                else:
+                    logging.error(f'key "{key_clean}" located in {md_file} has not been substituted')
+                    new_str = m.group(0)
+
+                md_str = md_str.replace(m.group(0), new_str)
+
+            with open(mdf.build_file, "w") as f:
+                f.write(md_str)
+
+    def _uniqueness_check(self, name):
+        error_msg = 'Table name "{name}" must be unique. This name is already used by {cont_type}="{container}"'
+
+        tbl = self.tables.get(name, None)
+        if tbl is not None:
+            raise ValueError(error_msg.format(name=name, cont_type="Table", container=tbl))
+        eq = self.equations.get(name, None)
+        if eq is not None:
+            raise ValueError(error_msg.format(name=name, cont_type="Equation", container=eq))
+        v = self.variables.get(name, None)
+        if v is not None:
+            raise ValueError(error_msg.format(name=name, cont_type="Variable", container=v))
 
     @property
     def main_dir(self):

src/paradoc/exceptions.py

@@ -0,0 +1,2 @@
+class LatexNotInstalled(Exception):
+    pass