From de340331ff34ad8b78cdb0089d2f54d7f16f752f Mon Sep 17 00:00:00 2001
From: Faisal Alquaddoomi <faisal.alquaddoomi@cuanschutz.edu>
Date: Wed, 25 Sep 2024 11:54:18 -0600
Subject: [PATCH 01/11] Replaced openai dependency with langchain_openai

---
 setup.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/setup.py b/setup.py
index b933cf9..3e89151 100644
--- a/setup.py
+++ b/setup.py
@@ -11,7 +11,7 @@
 
 setuptools.setup(
     name="manubot-ai-editor",
-    version="0.5.2",
+    version="0.5.3",
     author="Milton Pividori",
     author_email="miltondp@gmail.com",
     description="A Manubot plugin to revise a manuscript using GPT-3",
@@ -25,7 +25,8 @@
     ],
     python_requires=">=3.10",
     install_requires=[
-        "openai==0.28",
+        # "openai==0.28",
+        "langchain-openai==0.2.0",
         "pyyaml",
     ],
     classifiers=[

From ae19171eee44e7a64e6f72954af62efa37bd93af Mon Sep 17 00:00:00 2001
From: Faisal Alquaddoomi <faisal.alquaddoomi@cuanschutz.edu>
Date: Wed, 25 Sep 2024 12:24:58 -0600
Subject: [PATCH 02/11] For posterity, updates to latest release openai,
 updates code accordingly

---
 libs/manubot_ai_editor/models.py | 22 +++++++++++++---------
 setup.py                         |  3 ++-
 tests/test_model_basics.py       | 16 ++++++----------
 3 files changed, 21 insertions(+), 20 deletions(-)

diff --git a/libs/manubot_ai_editor/models.py b/libs/manubot_ai_editor/models.py
index c25dd68..a608542 100644
--- a/libs/manubot_ai_editor/models.py
+++ b/libs/manubot_ai_editor/models.py
@@ -5,7 +5,7 @@
 import time
 import json
 
-import openai
+from openai import OpenAI
 
 from manubot_ai_editor import env_vars
 
@@ -141,18 +141,22 @@ def __init__(
         super().__init__()
 
         # make sure the OpenAI API key is set
-        openai.api_key = openai_api_key
+        if openai_api_key is None:
+            # attempt to get the OpenAI API key from the environment, since one
+            # wasn't specified as an argument
+            openai_api_key = os.environ.get(env_vars.OPENAI_API_KEY, None)
 
-        if openai.api_key is None:
-            openai.api_key = os.environ.get(env_vars.OPENAI_API_KEY, None)
-
-            if openai.api_key is None or openai.api_key.strip() == "":
+            # if it's *still* not set, bail
+            if openai_api_key is None or openai_api_key.strip() == "":
                 raise ValueError(
                     f"OpenAI API key not found. Please provide it as parameter "
                     f"or set it as an the environment variable "
                     f"{env_vars.OPENAI_API_KEY}"
                 )
 
+        # construct the OpenAI client
+        self.client = OpenAI(api_key=openai_api_key)
+
         if env_vars.LANGUAGE_MODEL in os.environ:
             val = os.environ[env_vars.LANGUAGE_MODEL]
             if val.strip() != "":
@@ -527,11 +531,11 @@ def revise_paragraph(self, paragraph_text: str, section_name: str = None, resolv
                 )
 
                 if self.endpoint == "edits":
-                    completions = openai.Edit.create(**params)
+                    completions = self.client.edits.create(**params)
                 elif self.endpoint == "chat":
-                    completions = openai.ChatCompletion.create(**params)
+                    completions = self.client.chat.completions.create(**params)
                 else:
-                    completions = openai.Completion.create(**params)
+                    completions = self.client.completions.create(**params)
 
                 if self.endpoint == "chat":
                     message = completions.choices[0].message.content.strip()
diff --git a/setup.py b/setup.py
index 3e89151..ef67c0b 100644
--- a/setup.py
+++ b/setup.py
@@ -26,7 +26,8 @@
     python_requires=">=3.10",
     install_requires=[
         # "openai==0.28",
-        "langchain-openai==0.2.0",
+        "openai==1.48.0",
+        # "langchain-openai==0.2.0",
         "pyyaml",
     ],
     classifiers=[
diff --git a/tests/test_model_basics.py b/tests/test_model_basics.py
index 8242ca9..02545b5 100644
--- a/tests/test_model_basics.py
+++ b/tests/test_model_basics.py
@@ -32,12 +32,12 @@ def test_model_object_init_without_openai_api_key():
 
 @mock.patch.dict("os.environ", {env_vars.OPENAI_API_KEY: "env_var_test_value"})
 def test_model_object_init_with_openai_api_key_as_environment_variable():
-    GPT3CompletionModel(
+    model = GPT3CompletionModel(
         title="Test title",
         keywords=["test", "keywords"],
     )
 
-    assert models.openai.api_key == "env_var_test_value"
+    assert model.client.api_key == "env_var_test_value"
 
 
 def test_model_object_init_with_openai_api_key_as_parameter():
@@ -46,30 +46,26 @@ def test_model_object_init_with_openai_api_key_as_parameter():
         if env_vars.OPENAI_API_KEY in os.environ:
             os.environ.pop(env_vars.OPENAI_API_KEY)
 
-        GPT3CompletionModel(
+        model = GPT3CompletionModel(
             title="Test title",
             keywords=["test", "keywords"],
             openai_api_key="test_value",
         )
 
-        from manubot_ai_editor import models
-
-        assert models.openai.api_key == "test_value"
+        assert model.client.api_key == "test_value"
     finally:
         os.environ = _environ
 
 
 @mock.patch.dict("os.environ", {env_vars.OPENAI_API_KEY: "env_var_test_value"})
 def test_model_object_init_with_openai_api_key_as_parameter_has_higher_priority():
-    GPT3CompletionModel(
+    model = GPT3CompletionModel(
         title="Test title",
         keywords=["test", "keywords"],
         openai_api_key="test_value",
     )
 
-    from manubot_ai_editor import models
-
-    assert models.openai.api_key == "test_value"
+    assert model.client.api_key == "test_value"
 
 
 def test_model_object_init_default_language_model():

From 33d0adcddfb101d5bdb60351cf2ad9bfefc069cd Mon Sep 17 00:00:00 2001
From: Faisal Alquaddoomi <faisal.alquaddoomi@cuanschutz.edu>
Date: Wed, 25 Sep 2024 13:43:36 -0600
Subject: [PATCH 03/11] Switches from openai to langchain_openai, updates tests
 accordingly.

---
 libs/manubot_ai_editor/models.py | 71 ++++++++++++++++++++++++++------
 setup.py                         |  4 +-
 tests/test_model_basics.py       |  7 ++--
 3 files changed, 62 insertions(+), 20 deletions(-)

diff --git a/libs/manubot_ai_editor/models.py b/libs/manubot_ai_editor/models.py
index a608542..54714dd 100644
--- a/libs/manubot_ai_editor/models.py
+++ b/libs/manubot_ai_editor/models.py
@@ -5,7 +5,8 @@
 import time
 import json
 
-from openai import OpenAI
+from langchain_openai import OpenAI, ChatOpenAI
+from langchain_core.messages import BaseMessage, HumanMessage, SystemMessage
 
 from manubot_ai_editor import env_vars
 
@@ -154,9 +155,6 @@ def __init__(
                     f"{env_vars.OPENAI_API_KEY}"
                 )
 
-        # construct the OpenAI client
-        self.client = OpenAI(api_key=openai_api_key)
-
         if env_vars.LANGUAGE_MODEL in os.environ:
             val = os.environ[env_vars.LANGUAGE_MODEL]
             if val.strip() != "":
@@ -257,6 +255,22 @@ def __init__(
 
         self.several_spaces_pattern = re.compile(r"\s+")
 
+        if self.endpoint == "edits":
+            # FIXME: what's the "edits" equivalent in langchain?
+            client_cls = OpenAI
+        elif self.endpoint == "chat":
+            client_cls = ChatOpenAI
+        else:
+            client_cls = OpenAI
+
+        # construct the OpenAI client after all the rest of
+        # the settings above have been processed
+        self.client = client_cls(
+            api_key=openai_api_key,
+            **self.model_parameters,
+        )
+
+
     def get_prompt(
         self, paragraph_text: str, section_name: str = None, resolved_prompt: str = None
     ) -> str | tuple[str, str]:
@@ -530,17 +544,48 @@ def revise_paragraph(self, paragraph_text: str, section_name: str = None, resolv
                     flush=True,
                 )
 
-                if self.endpoint == "edits":
-                    completions = self.client.edits.create(**params)
-                elif self.endpoint == "chat":
-                    completions = self.client.chat.completions.create(**params)
+                # FIXME: 'params' contains a lot of fields that we're not
+                #  currently passing to the langchain client. i need to figure
+                #  out where they're supposed to be given, e.g. in the client
+                #  init or with each request.
+
+                # map the prompt to langchain's prompt types, based on what
+                # kind of endpoint we're using
+                if "messages" in params:
+                    # map the messages to langchain's message types
+                    # based on the 'role' field
+                    prompts = [
+                        HumanMessage(content=msg["content"])
+                        if msg["role"] == "user" else
+                        SystemMessage(content=msg["content"])
+                        for msg in params["messages"]
+                    ]
+                elif "instruction" in params:
+                    # since we don't know how to use the edits endpoint, we'll just
+                    # concatenate the instruction and input and use the regular
+                    # completion endpoint
+                    # FIXME: there's probably a langchain equivalent for
+                    #  "edits", so we should change this to use that
+                    prompts = [
+                        HumanMessage(content=params["instruction"]),
+                        HumanMessage(content=params["input"]),
+                    ]
+                elif "prompt" in params:
+                    prompts = [HumanMessage(content=params["prompt"])]
+
+                response = self.client.invoke(prompts)
+
+                if isinstance(response, BaseMessage):
+                    message = response.content.strip()
                 else:
-                    completions = self.client.completions.create(**params)
+                    message = response.strip()
+
+                # FIXME: the prior code retrieved the first of the 'choices'
+                #  response from the openai client. now, we only get one
+                #  response from the langchain client, but i should check
+                #  if that's really how langchain works or if there is a way
+                #  to get multiple 'choices' back from the backend.
 
-                if self.endpoint == "chat":
-                    message = completions.choices[0].message.content.strip()
-                else:
-                    message = completions.choices[0].text.strip()
             except Exception as e:
                 error_message = str(e)
                 print(f"Error: {error_message}")
diff --git a/setup.py b/setup.py
index ef67c0b..b17d981 100644
--- a/setup.py
+++ b/setup.py
@@ -25,9 +25,7 @@
     ],
     python_requires=">=3.10",
     install_requires=[
-        # "openai==0.28",
-        "openai==1.48.0",
-        # "langchain-openai==0.2.0",
+        "langchain-openai==0.2.0",
         "pyyaml",
     ],
     classifiers=[
diff --git a/tests/test_model_basics.py b/tests/test_model_basics.py
index 02545b5..54ec074 100644
--- a/tests/test_model_basics.py
+++ b/tests/test_model_basics.py
@@ -9,7 +9,6 @@
 import pytest
 
 from manubot_ai_editor.editor import ManuscriptEditor, env_vars
-from manubot_ai_editor import models
 from manubot_ai_editor.models import GPT3CompletionModel, RandomManuscriptRevisionModel
 
 MANUSCRIPTS_DIR = Path(__file__).parent / "manuscripts"
@@ -37,7 +36,7 @@ def test_model_object_init_with_openai_api_key_as_environment_variable():
         keywords=["test", "keywords"],
     )
 
-    assert model.client.api_key == "env_var_test_value"
+    assert model.client.openai_api_key.get_secret_value() == "env_var_test_value"
 
 
 def test_model_object_init_with_openai_api_key_as_parameter():
@@ -52,7 +51,7 @@ def test_model_object_init_with_openai_api_key_as_parameter():
             openai_api_key="test_value",
         )
 
-        assert model.client.api_key == "test_value"
+        assert model.client.openai_api_key.get_secret_value() == "test_value"
     finally:
         os.environ = _environ
 
@@ -65,7 +64,7 @@ def test_model_object_init_with_openai_api_key_as_parameter_has_higher_priority(
         openai_api_key="test_value",
     )
 
-    assert model.client.api_key == "test_value"
+    assert model.client.openai_api_key.get_secret_value() == "test_value"
 
 
 def test_model_object_init_default_language_model():

From 8e75813b5a1f34db02e609665d9d3b66c9315fba Mon Sep 17 00:00:00 2001
From: Faisal Alquaddoomi <faisal.alquaddoomi@cuanschutz.edu>
Date: Thu, 26 Sep 2024 08:39:29 -0600
Subject: [PATCH 04/11] Passed the remaining important(?) params, max_tokens
 and stop, to invoke()

---
 libs/manubot_ai_editor/models.py | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/libs/manubot_ai_editor/models.py b/libs/manubot_ai_editor/models.py
index 54714dd..7191e9f 100644
--- a/libs/manubot_ai_editor/models.py
+++ b/libs/manubot_ai_editor/models.py
@@ -544,17 +544,12 @@ def revise_paragraph(self, paragraph_text: str, section_name: str = None, resolv
                     flush=True,
                 )
 
-                # FIXME: 'params' contains a lot of fields that we're not
-                #  currently passing to the langchain client. i need to figure
-                #  out where they're supposed to be given, e.g. in the client
-                #  init or with each request.
-
                 # map the prompt to langchain's prompt types, based on what
                 # kind of endpoint we're using
                 if "messages" in params:
                     # map the messages to langchain's message types
                     # based on the 'role' field
-                    prompts = [
+                    prompt = [
                         HumanMessage(content=msg["content"])
                         if msg["role"] == "user" else
                         SystemMessage(content=msg["content"])
@@ -566,14 +561,18 @@ def revise_paragraph(self, paragraph_text: str, section_name: str = None, resolv
                     # completion endpoint
                     # FIXME: there's probably a langchain equivalent for
                     #  "edits", so we should change this to use that
-                    prompts = [
+                    prompt = [
                         HumanMessage(content=params["instruction"]),
                         HumanMessage(content=params["input"]),
                     ]
                 elif "prompt" in params:
-                    prompts = [HumanMessage(content=params["prompt"])]
+                    prompt = [HumanMessage(content=params["prompt"])]
 
-                response = self.client.invoke(prompts)
+                response = self.client.invoke(
+                    input=prompt,
+                    max_tokens=params.get("max_tokens"),
+                    stop=params.get("stop"),
+                )
 
                 if isinstance(response, BaseMessage):
                     message = response.content.strip()

From e4da6f071d025e6d9397e455e826c9724c7c1f7a Mon Sep 17 00:00:00 2001
From: Faisal Alquaddoomi <faisal.alquaddoomi@cuanschutz.edu>
Date: Thu, 26 Sep 2024 08:59:43 -0600
Subject: [PATCH 05/11] Changed langchain-openai dep to 0.2.x, so we get patch
 releases

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index b17d981..7f7e140 100644
--- a/setup.py
+++ b/setup.py
@@ -25,7 +25,7 @@
     ],
     python_requires=">=3.10",
     install_requires=[
-        "langchain-openai==0.2.0",
+        "langchain-openai~=0.2.0",
         "pyyaml",
     ],
     classifiers=[

From cdca3b862255d4a072a3cc3d361318bef678a381 Mon Sep 17 00:00:00 2001
From: Faisal Alquaddoomi <faisal.alquaddoomi@cuanschutz.edu>
Date: Thu, 26 Sep 2024 09:04:09 -0600
Subject: [PATCH 06/11] Added direct dependency on langchain-core~=0.3.6, since
 we use it directly in the code

---
 setup.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/setup.py b/setup.py
index 7f7e140..9b90a31 100644
--- a/setup.py
+++ b/setup.py
@@ -25,6 +25,7 @@
     ],
     python_requires=">=3.10",
     install_requires=[
+        "langchain-core~=0.3.6",
         "langchain-openai~=0.2.0",
         "pyyaml",
     ],

From 9a2d11b7977b12ff50c6e51f0c32d0800229cd77 Mon Sep 17 00:00:00 2001
From: Faisal Alquaddoomi <faisal.alquaddoomi@cuanschutz.edu>
Date: Wed, 23 Oct 2024 13:19:47 -0600
Subject: [PATCH 07/11] Ran black on models.py as suggested

---
 libs/manubot_ai_editor/models.py | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/libs/manubot_ai_editor/models.py b/libs/manubot_ai_editor/models.py
index 7191e9f..4096969 100644
--- a/libs/manubot_ai_editor/models.py
+++ b/libs/manubot_ai_editor/models.py
@@ -270,7 +270,6 @@ def __init__(
             **self.model_parameters,
         )
 
-
     def get_prompt(
         self, paragraph_text: str, section_name: str = None, resolved_prompt: str = None
     ) -> str | tuple[str, str]:
@@ -520,7 +519,9 @@ def get_params(self, paragraph_text, section_name, resolved_prompt=None):
 
         return params
 
-    def revise_paragraph(self, paragraph_text: str, section_name: str = None, resolved_prompt=None):
+    def revise_paragraph(
+        self, paragraph_text: str, section_name: str = None, resolved_prompt=None
+    ):
         """
         It revises a paragraph using GPT-3 completion model.
 
@@ -550,9 +551,11 @@ def revise_paragraph(self, paragraph_text: str, section_name: str = None, resolv
                     # map the messages to langchain's message types
                     # based on the 'role' field
                     prompt = [
-                        HumanMessage(content=msg["content"])
-                        if msg["role"] == "user" else
-                        SystemMessage(content=msg["content"])
+                        (
+                            HumanMessage(content=msg["content"])
+                            if msg["role"] == "user"
+                            else SystemMessage(content=msg["content"])
+                        )
                         for msg in params["messages"]
                     ]
                 elif "instruction" in params:
@@ -631,10 +634,10 @@ class DebuggingManuscriptRevisionModel(GPT3CompletionModel):
     """
 
     def __init__(self, *args, **kwargs):
-        if 'title' not in kwargs or kwargs['title'] is None:
-            kwargs['title'] = "Debugging Title"
-        if 'keywords' not in kwargs or kwargs['keywords'] is None:
-            kwargs['keywords'] = ["debugging", "keywords"]
+        if "title" not in kwargs or kwargs["title"] is None:
+            kwargs["title"] = "Debugging Title"
+        if "keywords" not in kwargs or kwargs["keywords"] is None:
+            kwargs["keywords"] = ["debugging", "keywords"]
 
         super().__init__(*args, **kwargs)
 

From bfacb162da1969c0865e85f085541d646a7dcb38 Mon Sep 17 00:00:00 2001
From: Faisal Alquaddoomi <faisal.alquaddoomi@cuanschutz.edu>
Date: Wed, 20 Nov 2024 14:38:14 -0700
Subject: [PATCH 08/11] Removes defunct 'edits' endpoint code, tests, and
 mentions in docs.

---
 libs/manubot_ai_editor/env_vars.py |  2 +-
 libs/manubot_ai_editor/models.py   | 47 +++++-------------------------
 tests/test_model_get_prompt.py     | 30 -------------------
 3 files changed, 8 insertions(+), 71 deletions(-)

diff --git a/libs/manubot_ai_editor/env_vars.py b/libs/manubot_ai_editor/env_vars.py
index 0ed9a06..a888bc6 100644
--- a/libs/manubot_ai_editor/env_vars.py
+++ b/libs/manubot_ai_editor/env_vars.py
@@ -16,7 +16,7 @@
 OPENAI_API_KEY = "OPENAI_API_KEY"
 
 # Language model to use. For example, "text-davinci-003", "gpt-3.5-turbo", "gpt-3.5-turbo-0301", etc
-# The tool currently supports the "chat/completions", "completions", and "edits" endpoints, and you can check
+# The tool currently supports the "chat/completions" and "completions" endpoints, and you can check
 # compatible models here: https://platform.openai.com/docs/models/model-endpoint-compatibility
 LANGUAGE_MODEL = "AI_EDITOR_LANGUAGE_MODEL"
 
diff --git a/libs/manubot_ai_editor/models.py b/libs/manubot_ai_editor/models.py
index 4096969..4a3c138 100644
--- a/libs/manubot_ai_editor/models.py
+++ b/libs/manubot_ai_editor/models.py
@@ -223,7 +223,7 @@ def __init__(
         self.title = title
         self.keywords = keywords if keywords is not None else []
 
-        # adjust options if edits or chat endpoint was selected
+        # adjust options if chat endpoint was selected
         self.endpoint = "chat"
 
         if model_engine.startswith(
@@ -231,9 +231,6 @@ def __init__(
         ):
             self.endpoint = "completions"
 
-            if "-edit-" in model_engine:
-                self.endpoint = "edits"
-
         print(f"Language model: {model_engine}")
         print(f"Model endpoint used: {self.endpoint}")
 
@@ -255,10 +252,7 @@ def __init__(
 
         self.several_spaces_pattern = re.compile(r"\s+")
 
-        if self.endpoint == "edits":
-            # FIXME: what's the "edits" equivalent in langchain?
-            client_cls = OpenAI
-        elif self.endpoint == "chat":
+        if self.endpoint == "chat":
             client_cls = ChatOpenAI
         else:
             client_cls = OpenAI
@@ -285,13 +279,9 @@ def get_prompt(
             resolved_prompt: prompt resolved via ai-revision config, if available
 
         Returns:
-            If self.endpoint != "edits", then returns a string with the prompt to be used by the model for the revision of the paragraph.
+            A string with the prompt to be used by the model for the revision of the paragraph.
             It contains two paragraphs of text: the command for the model
             ("Revise...") and the paragraph to revise.
-
-            If self.endpoint == "edits", then returns a tuple with two strings:
-             1) the instructions to be used by the model for the revision of the paragraph,
-             2) the paragraph to revise.
         """
 
         # prompts are resolved in the following order, with the first satisfied
@@ -327,8 +317,6 @@ def get_prompt(
                 f"Using custom prompt from environment variable '{env_vars.CUSTOM_PROMPT}'"
             )
 
-            # FIXME: if {paragraph_text} is in the prompt, this won't work for the edits endpoint
-            #  a simple workaround is to remove {paragraph_text} from the prompt
             prompt = custom_prompt.format(**placeholders)
         elif resolved_prompt:
             # use the resolved prompt from the ai-revision config files, if available
@@ -401,14 +389,10 @@ def get_prompt(
         if custom_prompt is None:
             prompt = self.several_spaces_pattern.sub(" ", prompt).strip()
 
-        if self.endpoint != "edits":
-            if custom_prompt is not None and "{paragraph_text}" in custom_prompt:
-                return prompt
+        if custom_prompt is not None and "{paragraph_text}" in custom_prompt:
+            return prompt
 
-            return f"{prompt}.\n\n{paragraph_text.strip()}"
-        else:
-            prompt = prompt.replace("the following paragraph", "this paragraph")
-            return f"{prompt}.", paragraph_text.strip()
+        return f"{prompt}.\n\n{paragraph_text.strip()}"
 
     def get_max_tokens(self, paragraph_text: str, fraction: float = 2.0) -> int:
         """
@@ -489,14 +473,7 @@ def get_params(self, paragraph_text, section_name, resolved_prompt=None):
             "n": 1,
         }
 
-        if self.endpoint == "edits":
-            params.update(
-                {
-                    "instruction": prompt[0],
-                    "input": prompt[1],
-                }
-            )
-        elif self.endpoint == "chat":
+        if self.endpoint == "chat":
             params.update(
                 {
                     "messages": [
@@ -558,16 +535,6 @@ def revise_paragraph(
                         )
                         for msg in params["messages"]
                     ]
-                elif "instruction" in params:
-                    # since we don't know how to use the edits endpoint, we'll just
-                    # concatenate the instruction and input and use the regular
-                    # completion endpoint
-                    # FIXME: there's probably a langchain equivalent for
-                    #  "edits", so we should change this to use that
-                    prompt = [
-                        HumanMessage(content=params["instruction"]),
-                        HumanMessage(content=params["input"]),
-                    ]
                 elif "prompt" in params:
                     prompt = [HumanMessage(content=params["prompt"])]
 
diff --git a/tests/test_model_get_prompt.py b/tests/test_model_get_prompt.py
index 538e654..438a16d 100644
--- a/tests/test_model_get_prompt.py
+++ b/tests/test_model_get_prompt.py
@@ -28,36 +28,6 @@ def test_get_prompt_for_abstract():
     assert "  " not in prompt
 
 
-def test_get_prompt_for_abstract_edit_endpoint():
-    manuscript_title = "Title of the manuscript to be revised"
-    manuscript_keywords = ["keyword0", "keyword1", "keyword2"]
-
-    model = GPT3CompletionModel(
-        title=manuscript_title,
-        keywords=manuscript_keywords,
-        model_engine="text-davinci-edit-001",
-    )
-
-    paragraph_text = "Text of the abstract. "
-
-    instruction, paragraph = model.get_prompt(paragraph_text, "abstract")
-    assert instruction is not None
-    assert isinstance(instruction, str)
-    assert paragraph is not None
-    assert isinstance(paragraph, str)
-
-    assert "this paragraph" in instruction
-    assert "abstract" in instruction
-    assert f"'{manuscript_title}'" in instruction
-    assert f"{manuscript_keywords[0]}" in instruction
-    assert f"{manuscript_keywords[1]}" in instruction
-    assert f"{manuscript_keywords[2]}" in instruction
-    assert "  " not in instruction
-    assert instruction.startswith("Revise")
-
-    assert paragraph_text.strip() == paragraph
-
-
 def test_get_prompt_for_introduction():
     manuscript_title = "Title of the manuscript to be revised"
     manuscript_keywords = ["keyword0", "keyword1", "keyword2"]

From 3bafcf6bd0b79460a41b4758e63ebbc748b3b408 Mon Sep 17 00:00:00 2001
From: Faisal Alquaddoomi <faisal.alquaddoomi@cuanschutz.edu>
Date: Wed, 20 Nov 2024 14:38:57 -0700
Subject: [PATCH 09/11] Adds docstring to get_params(), other small comment and
 consistency tweaks

---
 libs/manubot_ai_editor/models.py | 24 +++++++++++++++++++++---
 1 file changed, 21 insertions(+), 3 deletions(-)

diff --git a/libs/manubot_ai_editor/models.py b/libs/manubot_ai_editor/models.py
index 4a3c138..0944c7f 100644
--- a/libs/manubot_ai_editor/models.py
+++ b/libs/manubot_ai_editor/models.py
@@ -466,6 +466,22 @@ def get_max_tokens_from_error_message(error_message: str) -> dict[str, int] | No
         }
 
     def get_params(self, paragraph_text, section_name, resolved_prompt=None):
+        """
+        Given the paragraph text and section name, produces parameters that are
+        used when invoking an LLM via an API.
+
+        The specific parameters vary depending on the endpoint being used, which
+        is determined by the model that was chosen when GPT3CompletionModel was
+        instantiated.
+
+        Args:
+            paragraph_text: The text of the paragraph to be revised.
+            section_name: The name of the section the paragraph belongs to.
+            resolved_prompt: The prompt resolved via ai-revision config files, if available.
+
+        Returns:
+            A dictionary of parameters to be used when invoking an LLM API.
+        """
         max_tokens = self.get_max_tokens(paragraph_text)
         prompt = self.get_prompt(paragraph_text, section_name, resolved_prompt)
 
@@ -504,13 +520,15 @@ def revise_paragraph(
 
         Arguments:
             paragraph_text (str): Paragraph text to revise.
-            section_name (str): Section name of the paragraph.
-            throw_error (bool): If True, it throws an error if the API call fails.
-                If False, it returns the original paragraph text.
+            section_name (str): Section name of the paragrap
+            resolved_prompt (str): Prompt resolved via ai-revision config files, if available.
 
         Returns:
             Revised paragraph text.
         """
+
+        # based on the paragraph text to revise and the section to which it
+        # belongs, constructs parameters that we'll use to query the LLM's API
         params = self.get_params(paragraph_text, section_name, resolved_prompt)
 
         retry_count = 0

From a98f69ae9e6222dae2dce7b296cfd5bfe1aac931 Mon Sep 17 00:00:00 2001
From: Faisal Alquaddoomi <faisal.alquaddoomi@cuanschutz.edu>
Date: Wed, 20 Nov 2024 14:39:19 -0700
Subject: [PATCH 10/11] Formatted code w/black

---
 libs/manubot_ai_editor/prompt_config.py | 20 +++---
 tests/test_editor.py                    | 20 +++---
 tests/test_prompt_config.py             | 94 +++++++++++++++++--------
 3 files changed, 85 insertions(+), 49 deletions(-)

diff --git a/libs/manubot_ai_editor/prompt_config.py b/libs/manubot_ai_editor/prompt_config.py
index d2d9f6e..695952e 100644
--- a/libs/manubot_ai_editor/prompt_config.py
+++ b/libs/manubot_ai_editor/prompt_config.py
@@ -47,9 +47,9 @@ def __init__(self, config_dir: str | Path, title: str, keywords: str) -> None:
         # specify filename-to-prompt mappings; if both are present, we use
         # self.config.files, but warn the user that they should only use one
         if (
-            self.prompts_files is not None and
-            self.config is not None and
-            self.config.get('files', {}).get('matchings') is not None
+            self.prompts_files is not None
+            and self.config is not None
+            and self.config.get("files", {}).get("matchings") is not None
         ):
             print(
                 "WARNING: Both 'ai-revision-config.yaml' and 'ai-revision-prompts.yaml' specify filename-to-prompt mappings. "
@@ -93,7 +93,7 @@ def _load_custom_prompts(self) -> tuple[dict, dict]:
         # same as _load_config, if no config folder was specified, we just
         if self.config_dir is None:
             return (None, None)
-        
+
         prompt_file_path = os.path.join(self.config_dir, "ai-revision-prompts.yaml")
 
         try:
@@ -150,7 +150,7 @@ def get_prompt_for_filename(
         # ai-revision-prompts.yaml specifies prompts_files, then files.matchings
         # takes precedence.
         # (the user is notified of this in a validation warning in __init__)
-        
+
         # then, consult ai-revision-config.yaml's 'matchings' collection if a
         # match is found, use the prompt ai-revision-prompts.yaml
         for entry in get_obj_path(self.config, ("files", "matchings"), missing=[]):
@@ -169,7 +169,10 @@ def get_prompt_for_filename(
                         if resolved_prompt is not None:
                             resolved_prompt = resolved_prompt.strip()
 
-                    return ( resolved_prompt, m, )
+                    return (
+                        resolved_prompt,
+                        m,
+                    )
 
         # since we haven't found a match yet, consult ai-revision-prompts.yaml's
         # 'prompts_files' collection
@@ -185,11 +188,10 @@ def get_prompt_for_filename(
         resolved_default_prompt = None
         if use_default and self.prompts is not None:
             resolved_default_prompt = self.prompts.get(
-                get_obj_path(self.config, ("files", "default_prompt")),
-                None
+                get_obj_path(self.config, ("files", "default_prompt")), None
             )
 
             if resolved_default_prompt is not None:
                 resolved_default_prompt = resolved_default_prompt.strip()
-        
+
         return (resolved_default_prompt, None)
diff --git a/tests/test_editor.py b/tests/test_editor.py
index 60bb778..1068a6a 100644
--- a/tests/test_editor.py
+++ b/tests/test_editor.py
@@ -610,9 +610,7 @@ def test_revise_methods_with_equation_that_was_alrady_revised(
         # GPT3CompletionModel(None, None),
     ],
 )
-def test_revise_methods_mutator_epistasis_paper(
-    tmp_path, model, filename
-):
+def test_revise_methods_mutator_epistasis_paper(tmp_path, model, filename):
     """
     This papers has several test cases:
      - it ends with multiple blank lines
@@ -635,7 +633,7 @@ def test_revise_methods_mutator_epistasis_paper(
     )
 
     assert (
-            r"""
+        r"""
 %%% PARAGRAPH START %%%
 Briefly, we identified private single-nucleotide mutations in each BXD that were absent from all other BXDs, as well as from the C57BL/6J and DBA/2J parents.
 We required each private variant to be meet the following criteria:
@@ -651,11 +649,11 @@ def test_revise_methods_mutator_epistasis_paper(
 * must occur on a parental haplotype that was inherited by at least one other BXD at the same locus; these other BXDs must be homozygous for the reference allele at the variant site
 %%% PARAGRAPH END %%%
         """.strip()
-            in open(tmp_path / filename).read()
+        in open(tmp_path / filename).read()
     )
-    
+
     assert (
-            r"""
+        r"""
 ### Extracting mutation signatures 
 
 We used SigProfilerExtractor (v.1.1.21) [@PMID:30371878] to extract mutation signatures from the BXD mutation data.
@@ -678,11 +676,11 @@ def test_revise_methods_mutator_epistasis_paper(
 
 ### Comparing mutation spectra between Mouse Genomes Project strains
         """.strip()
-            in open(tmp_path / filename).read()
+        in open(tmp_path / filename).read()
     )
-    
+
     assert (
-            r"""
+        r"""
 %%% PARAGRAPH START %%%
 We investigated the region implicated by our aggregate mutation spectrum distance approach on chromosome 6 by subsetting the joint-genotyped BXD VCF file (European Nucleotide Archive accession PRJEB45429 [@url:https://www.ebi.ac.uk/ena/browser/view/PRJEB45429]) using `bcftools` [@PMID:33590861].
 We defined the candidate interval surrounding the cosine distance peak on chromosome 6 as the 90% bootstrap confidence interval (extending from approximately 95 Mbp to 114 Mbp).
@@ -693,7 +691,7 @@ def test_revise_methods_mutator_epistasis_paper(
  java -Xmx16g -jar /path/to/snpeff/jarfile GRCm38.75 /path/to/bxd/vcf > /path/to/uncompressed/output/vcf
 ```
         """.strip()
-            in open(tmp_path / filename).read()
+        in open(tmp_path / filename).read()
     )
 
 
diff --git a/tests/test_prompt_config.py b/tests/test_prompt_config.py
index 7f68702..4d32b6a 100644
--- a/tests/test_prompt_config.py
+++ b/tests/test_prompt_config.py
@@ -5,7 +5,7 @@
 from manubot_ai_editor.models import (
     GPT3CompletionModel,
     RandomManuscriptRevisionModel,
-    DebuggingManuscriptRevisionModel
+    DebuggingManuscriptRevisionModel,
 )
 from manubot_ai_editor.prompt_config import IGNORE_FILE
 import pytest
@@ -13,7 +13,9 @@
 from utils.dir_union import mock_unify_open
 
 MANUSCRIPTS_DIR = Path(__file__).parent / "manuscripts" / "phenoplier_full" / "content"
-MANUSCRIPTS_CONFIG_DIR = Path(__file__).parent / "manuscripts" / "phenoplier_full" / "ci"
+MANUSCRIPTS_CONFIG_DIR = (
+    Path(__file__).parent / "manuscripts" / "phenoplier_full" / "ci"
+)
 
 
 # check that this path exists and resolve it
@@ -42,7 +44,9 @@ def test_create_manuscript_editor():
 
 
 # check that we can resolve a file to a prompt, and that it's the correct prompt
-@mock.patch("builtins.open", mock_unify_open(MANUSCRIPTS_CONFIG_DIR, PHENOPLIER_PROMPTS_DIR))
+@mock.patch(
+    "builtins.open", mock_unify_open(MANUSCRIPTS_CONFIG_DIR, PHENOPLIER_PROMPTS_DIR)
+)
 def test_resolve_prompt():
     content_dir = MANUSCRIPTS_DIR.resolve(strict=True)
     config_dir = MANUSCRIPTS_CONFIG_DIR.resolve(strict=True)
@@ -100,7 +104,9 @@ def test_resolve_prompt():
 
 # test that we get the default prompt with a None match object for a
 # file we don't recognize
-@mock.patch("builtins.open", mock_unify_open(MANUSCRIPTS_CONFIG_DIR, PHENOPLIER_PROMPTS_DIR))
+@mock.patch(
+    "builtins.open", mock_unify_open(MANUSCRIPTS_CONFIG_DIR, PHENOPLIER_PROMPTS_DIR)
+)
 def test_resolve_default_prompt_unknown_file():
     content_dir = MANUSCRIPTS_DIR.resolve(strict=True)
     config_dir = MANUSCRIPTS_CONFIG_DIR.resolve(strict=True)
@@ -114,7 +120,9 @@ def test_resolve_default_prompt_unknown_file():
 
 # check that a file we don't recognize gets match==None and the 'default' prompt
 # from the ai-revision-config.yaml file
-@mock.patch("builtins.open", mock_unify_open(MANUSCRIPTS_CONFIG_DIR, PHENOPLIER_PROMPTS_DIR))
+@mock.patch(
+    "builtins.open", mock_unify_open(MANUSCRIPTS_CONFIG_DIR, PHENOPLIER_PROMPTS_DIR)
+)
 def test_unresolved_gets_default_prompt():
     content_dir = MANUSCRIPTS_DIR.resolve(strict=True)
     config_dir = MANUSCRIPTS_CONFIG_DIR.resolve(strict=True)
@@ -150,7 +158,9 @@ def test_unresolved_gets_default_prompt():
 # - Both ai-revision-config.yaml and ai-revision-prompts.yaml specify filename matchings
 #   (conflicting_promptsfiles_matchings)
 CONFLICTING_PROMPTSFILES_MATCHINGS_DIR = (
-    Path(__file__).parent / "config_loader_fixtures" / "conflicting_promptsfiles_matchings"
+    Path(__file__).parent
+    / "config_loader_fixtures"
+    / "conflicting_promptsfiles_matchings"
 )
 # ---
 # test ManuscriptEditor.prompt_config sub-attributes are set correctly
@@ -178,7 +188,9 @@ def test_no_config_unloaded():
     assert editor.prompt_config.config is None
 
 
-@mock.patch("builtins.open", mock_unify_open(MANUSCRIPTS_CONFIG_DIR, ONLY_REV_PROMPTS_DIR))
+@mock.patch(
+    "builtins.open", mock_unify_open(MANUSCRIPTS_CONFIG_DIR, ONLY_REV_PROMPTS_DIR)
+)
 def test_only_rev_prompts_loaded():
     editor = get_editor()
 
@@ -188,7 +200,9 @@ def test_only_rev_prompts_loaded():
     assert editor.prompt_config.config is None
 
 
-@mock.patch("builtins.open", mock_unify_open(MANUSCRIPTS_CONFIG_DIR, BOTH_PROMPTS_CONFIG_DIR))
+@mock.patch(
+    "builtins.open", mock_unify_open(MANUSCRIPTS_CONFIG_DIR, BOTH_PROMPTS_CONFIG_DIR)
+)
 def test_both_prompts_loaded():
     editor = get_editor()
 
@@ -211,7 +225,8 @@ def test_single_generic_loaded():
 
 
 @mock.patch(
-    "builtins.open", mock_unify_open(MANUSCRIPTS_CONFIG_DIR, CONFLICTING_PROMPTSFILES_MATCHINGS_DIR)
+    "builtins.open",
+    mock_unify_open(MANUSCRIPTS_CONFIG_DIR, CONFLICTING_PROMPTSFILES_MATCHINGS_DIR),
 )
 def test_conflicting_sources_warning(capfd):
     """
@@ -234,7 +249,7 @@ def test_conflicting_sources_warning(capfd):
     # for this test, we define both prompts_files and files.matchings which
     # creates a conflict that produces the warning we're looking for
     assert editor.prompt_config.prompts_files is not None
-    assert editor.prompt_config.config['files']['matchings'] is not None
+    assert editor.prompt_config.config["files"]["matchings"] is not None
 
     expected_warning = (
         "WARNING: Both 'ai-revision-config.yaml' and "
@@ -262,11 +277,13 @@ def test_conflicting_sources_warning(capfd):
         RandomManuscriptRevisionModel(),
         DebuggingManuscriptRevisionModel(
             title="Test title", keywords=["test", "keywords"]
-        )
+        ),
         # GPT3CompletionModel(None, None),
     ],
 )
-@mock.patch("builtins.open", mock_unify_open(MANUSCRIPTS_CONFIG_DIR, BOTH_PROMPTS_CONFIG_DIR))
+@mock.patch(
+    "builtins.open", mock_unify_open(MANUSCRIPTS_CONFIG_DIR, BOTH_PROMPTS_CONFIG_DIR)
+)
 def test_revise_entire_manuscript(tmp_path, model):
     print(f"\n{str(tmp_path)}\n")
     me = get_editor()
@@ -284,7 +301,9 @@ def test_revise_entire_manuscript(tmp_path, model):
     assert len(output_md_files) == 9
 
 
-@mock.patch("builtins.open", mock_unify_open(MANUSCRIPTS_CONFIG_DIR, BOTH_PROMPTS_CONFIG_DIR))
+@mock.patch(
+    "builtins.open", mock_unify_open(MANUSCRIPTS_CONFIG_DIR, BOTH_PROMPTS_CONFIG_DIR)
+)
 def test_revise_entire_manuscript_includes_title_keywords(tmp_path):
     from os.path import basename
 
@@ -317,8 +336,12 @@ def test_revise_entire_manuscript_includes_title_keywords(tmp_path):
 
         with open(output_md_file, "r") as f:
             content = f.read()
-            assert me.title in content, f"not found in filename: {basename(output_md_file)}"
-            assert ", ".join(me.keywords) in content, f"not found in filename: {basename(output_md_file)}"
+            assert (
+                me.title in content
+            ), f"not found in filename: {basename(output_md_file)}"
+            assert (
+                ", ".join(me.keywords) in content
+            ), f"not found in filename: {basename(output_md_file)}"
 
 
 # ==============================================================================
@@ -329,7 +352,11 @@ def test_revise_entire_manuscript_includes_title_keywords(tmp_path):
     Path(__file__).parent / "config_loader_fixtures" / "prompt_propogation"
 )
 
-@mock.patch("builtins.open", mock_unify_open(MANUSCRIPTS_CONFIG_DIR, PROMPT_PROPOGATION_CONFIG_DIR))
+
+@mock.patch(
+    "builtins.open",
+    mock_unify_open(MANUSCRIPTS_CONFIG_DIR, PROMPT_PROPOGATION_CONFIG_DIR),
+)
 def test_prompts_in_final_result(tmp_path):
     """
     Tests that the prompts are making it into the final resulting .md files.
@@ -348,9 +375,7 @@ def test_prompts_in_final_result(tmp_path):
     """
     me = get_editor()
 
-    model = DebuggingManuscriptRevisionModel(
-        title=me.title, keywords=me.keywords
-    )
+    model = DebuggingManuscriptRevisionModel(title=me.title, keywords=me.keywords)
 
     output_folder = tmp_path
     assert output_folder.exists()
@@ -361,7 +386,8 @@ def test_prompts_in_final_result(tmp_path):
     files_to_prompts = {
         "00.front-matter.md": "This is the front-matter prompt.",
         "01.abstract.md": "This is the abstract prompt",
-        "02.introduction.md": "This is the introduction prompt for the paper titled '%s'." % me.title,
+        "02.introduction.md": "This is the introduction prompt for the paper titled '%s'."
+        % me.title,
         # "04.00.results.md": "This is the results prompt",
         "04.05.00.results_framework.md": "This is the results_framework prompt",
         "04.05.01.crispr.md": "This is the crispr prompt",
@@ -389,15 +415,26 @@ def test_prompts_in_final_result(tmp_path):
 
 # to save on time/cost, we use a version of the phenoplier manuscript that only
 # contains the first paragraph of each section
-BRIEF_MANUSCRIPTS_DIR = Path(__file__).parent / "manuscripts" / "phenoplier_full_only_first_para" / "content"
-BRIEF_MANUSCRIPTS_CONFIG_DIR = Path(__file__).parent / "manuscripts" / "phenoplier_full_only_first_para" / "ci"
+BRIEF_MANUSCRIPTS_DIR = (
+    Path(__file__).parent
+    / "manuscripts"
+    / "phenoplier_full_only_first_para"
+    / "content"
+)
+BRIEF_MANUSCRIPTS_CONFIG_DIR = (
+    Path(__file__).parent / "manuscripts" / "phenoplier_full_only_first_para" / "ci"
+)
 
 PROMPT_PROPOGATION_CONFIG_DIR = (
     Path(__file__).parent / "config_loader_fixtures" / "prompt_gpt3_e2e"
 )
 
+
 @pytest.mark.cost
-@mock.patch("builtins.open", mock_unify_open(BRIEF_MANUSCRIPTS_CONFIG_DIR, PROMPT_PROPOGATION_CONFIG_DIR))
+@mock.patch(
+    "builtins.open",
+    mock_unify_open(BRIEF_MANUSCRIPTS_CONFIG_DIR, PROMPT_PROPOGATION_CONFIG_DIR),
+)
 def test_prompts_apply_gpt3(tmp_path):
     """
     Tests that the custom prompts are applied when actually applying
@@ -408,16 +445,15 @@ def test_prompts_apply_gpt3(tmp_path):
     this test is marked 'cost' and requires the --runcost argument to be run,
     e.g. to run just this test: `pytest --runcost -k test_prompts_apply_gpt3`.
 
-    As with test_prompts_in_final_result above, files that have no input and 
+    As with test_prompts_in_final_result above, files that have no input and
     thus no applied prompt are ignored.
     """
-    me = get_editor(content_dir=BRIEF_MANUSCRIPTS_DIR, config_dir=BRIEF_MANUSCRIPTS_CONFIG_DIR)
-
-    model = GPT3CompletionModel(
-        title=me.title,
-        keywords=me.keywords
+    me = get_editor(
+        content_dir=BRIEF_MANUSCRIPTS_DIR, config_dir=BRIEF_MANUSCRIPTS_CONFIG_DIR
     )
 
+    model = GPT3CompletionModel(title=me.title, keywords=me.keywords)
+
     output_folder = tmp_path
     assert output_folder.exists()
 

From 4c66a58de9e1bc1d5271cdc5e3697f62c33e9b10 Mon Sep 17 00:00:00 2001
From: Faisal Alquaddoomi <faisal.alquaddoomi@cuanschutz.edu>
Date: Tue, 3 Dec 2024 14:13:23 -0700
Subject: [PATCH 11/11] Removed FIXME; we'll always use a number of responses,
 aka n, of 1 so no need to use call() over invoke()

---
 libs/manubot_ai_editor/models.py | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/libs/manubot_ai_editor/models.py b/libs/manubot_ai_editor/models.py
index 0944c7f..80a2dcc 100644
--- a/libs/manubot_ai_editor/models.py
+++ b/libs/manubot_ai_editor/models.py
@@ -567,12 +567,6 @@ def revise_paragraph(
                 else:
                     message = response.strip()
 
-                # FIXME: the prior code retrieved the first of the 'choices'
-                #  response from the openai client. now, we only get one
-                #  response from the langchain client, but i should check
-                #  if that's really how langchain works or if there is a way
-                #  to get multiple 'choices' back from the backend.
-
             except Exception as e:
                 error_message = str(e)
                 print(f"Error: {error_message}")