From a8dc90054098d8763f628af29a4e852c4f320ac7 Mon Sep 17 00:00:00 2001
From: Khoroshevskyi <sasha99250@gmail.com>
Date: Mon, 11 Dec 2023 14:28:56 -0500
Subject: [PATCH] fixed docs and added from_pep_config method

---
 docs/initialize.md    | 27 +++++++++++++++++++++------
 peppy/project.py      | 31 +++++++++++++++++++++++++++++++
 peppy/utils.py        |  1 -
 tests/test_Project.py |  4 ++++
 4 files changed, 56 insertions(+), 7 deletions(-)

diff --git a/docs/initialize.md b/docs/initialize.md
index 1ae33c8a..a762045e 100644
--- a/docs/initialize.md
+++ b/docs/initialize.md
@@ -7,13 +7,13 @@ Additionally, peppy can be initiated using Python objects such as a pandas dataf
 ## 1. Using a configuration file
 ```python
 import peppy
-project = peppy.Project("path/to/project/config.yaml")
+project = peppy.Project.from_pep_config("path/to/project/config.yaml")
 ```
 
 ## 2. Using csv file (sample sheet)
 ```python
 import peppy
-project = peppy.Project("path/to/project/sample_sheet.csv")
+project = peppy.Project.from_pep_config("path/to/project/sample_sheet.csv")
 ```
 
 ## 3. Using yaml sample sheet
@@ -34,13 +34,28 @@ project = peppy.Project.from_pandas(df)
 ## 5. Using a peppy generated dict
 ```python
 import peppy
-project = peppy.Project.from_dict({`_config`: str,
-                                   `_samples`: list | dict,
-                                   `_subsamples`: list[list | dict]})
+project = peppy.Project.from_dict(
+    {'_config': {'description': None,
+                 'name': 'example_basic',
+                 'pep_version': '2.0.0',
+                 'sample_table': 'sample_table.csv',},
+    '_sample_dict': [{'organism': 'pig', 'sample_name': 'pig_0h', 'time': '0'},
+                     {'organism': 'pig', 'sample_name': 'pig_1h', 'time': '1'},
+                     {'organism': 'frog', 'sample_name': 'frog_0h', 'time': '0'},
+                     {'organism': 'frog', 'sample_name': 'frog_1h', 'time': '1'}],
+    '_subsample_list': [[{'read1': 'frog1a_data.txt',
+                       'read2': 'frog1a_data2.txt',
+                       'sample_name': 'frog_0h'},
+                      {'read1': 'frog1b_data.txt',
+                       'read2': 'frog1b_data2.txt',
+                       'sample_name': 'pig_0h'},
+                      {'read1': 'frog1c_data.txt',
+                       'read2': 'frog1b_data2.txt',
+                       'sample_name': 'pig_0h'}]]})
 ```
 
 ## 6. Using a csv file from a url
 ```python
 import peppy
-project = peppy.Project("example_url.csv")
+project = peppy.Project("https://raw.githubusercontent.com/pepkit/example_peps/master/example_basic/sample_table.csv")
 ```
diff --git a/peppy/project.py b/peppy/project.py
index 742565a7..5fe05822 100644
--- a/peppy/project.py
+++ b/peppy/project.py
@@ -235,6 +235,37 @@ def from_dict(cls, pep_dictionary: dict):
 
         return tmp_obj
 
+    @classmethod
+    def from_pep_config(
+        cls,
+        cfg: str = None,
+        amendments: Union[str, Iterable[str]] = None,
+        sample_table_index: Union[str, Iterable[str]] = None,
+        subsample_table_index: Union[str, Iterable[str]] = None,
+        defer_samples_creation: bool = False,
+    ):
+        """
+        Init a peppy project instance from a yaml file
+
+        :param str cfg: Project config file (YAML) or sample table (CSV/TSV)
+            with one row per sample to constitute project
+        :param str | Iterable[str] sample_table_index: name of the columns to set
+            the sample_table index to
+        :param str | Iterable[str] subsample_table_index: name of the columns to set
+            the subsample_table index to
+        :param str | Iterable[str] amendments: names of the amendments to activate
+        :param Iterable[str] amendments: amendments to use within configuration file
+        :param bool defer_samples_creation: whether the sample creation should be skipped
+        """
+        # TODO: this is just a copy of the __init__ method. It should be refactored
+        return cls(
+            cfg=cfg,
+            amendments=amendments,
+            sample_table_index=sample_table_index,
+            subsample_table_index=subsample_table_index,
+            defer_samples_creation=defer_samples_creation,
+        )
+
     @classmethod
     def from_yaml(cls, yaml_file: str):
         """
diff --git a/peppy/utils.py b/peppy/utils.py
index e4fed739..35e6017a 100644
--- a/peppy/utils.py
+++ b/peppy/utils.py
@@ -5,7 +5,6 @@
 from typing import Dict, Mapping
 from urllib.request import urlopen
 
-import yacman
 import yaml
 from ubiquerg import expandpath, is_url
 
diff --git a/tests/test_Project.py b/tests/test_Project.py
index 685d7259..4aa14b27 100644
--- a/tests/test_Project.py
+++ b/tests/test_Project.py
@@ -350,6 +350,10 @@ def test_from_dict_instatiation(self, example_pep_cfg_path):
         representation.
         """
         p1 = Project(cfg=example_pep_cfg_path)
+        ff = p1.to_dict(extended=True)
+        import pprint
+
+        pprint.pprint(ff)
         p2 = Project.from_dict(p1.to_dict(extended=True))
         assert p1 == p2