diff --git a/docs/api.md b/docs/api.md
deleted file mode 100644
index fe7f6fdd1561d82e13f11d38fbb842b5dcbcb87e..0000000000000000000000000000000000000000
--- a/docs/api.md
+++ /dev/null
@@ -1,540 +0,0 @@
-<a id="__init__"></a>
-
-# \_\_init\_\_
-
-<a id="__main__"></a>
-
-# \_\_main\_\_
-
-<a id="util"></a>
-
-# util
-
-<a id="logging_config"></a>
-
-# logging\_config
-
-<a id="logging_config.setup_logger"></a>
-
-#### setup\_logger
-
-```python
-def setup_logger(log_level: int = logging.INFO)
-```
-
-Sets up logger as a singleton outputing to file and sysout syserr
-
-<a id="logging_config.set_log_level"></a>
-
-#### set\_log\_level
-
-```python
-def set_log_level(log_level: int)
-```
-
-Sets the log level for the acmc logger
-
-<a id="main"></a>
-
-# main
-
-<a id="main.trud_install"></a>
-
-#### trud\_install
-
-```python
-def trud_install(args: argparse.Namespace)
-```
-
-Handle the `trud install` command.
-
-<a id="main.omop_install"></a>
-
-#### omop\_install
-
-```python
-def omop_install(args: argparse.Namespace)
-```
-
-Handle the `omop install` command.
-
-<a id="main.omop_clear"></a>
-
-#### omop\_clear
-
-```python
-def omop_clear(args: argparse.Namespace)
-```
-
-Handle the `omop clear` command.
-
-<a id="main.omop_delete"></a>
-
-#### omop\_delete
-
-```python
-def omop_delete(args: argparse.Namespace)
-```
-
-Handle the `omop delete` command.
-
-<a id="main.phen_init"></a>
-
-#### phen\_init
-
-```python
-def phen_init(args: argparse.Namespace)
-```
-
-Handle the `phen init` command.
-
-<a id="main.phen_fork"></a>
-
-#### phen\_fork
-
-```python
-def phen_fork(args: argparse.Namespace)
-```
-
-Handle the `phen fork` command.
-
-<a id="main.phen_validate"></a>
-
-#### phen\_validate
-
-```python
-def phen_validate(args: argparse.Namespace)
-```
-
-Handle the `phen validate` command.
-
-<a id="main.phen_map"></a>
-
-#### phen\_map
-
-```python
-def phen_map(args: argparse.Namespace)
-```
-
-Handle the `phen map` command.
-
-<a id="main.phen_export"></a>
-
-#### phen\_export
-
-```python
-def phen_export(args: argparse.Namespace)
-```
-
-Handle the `phen copy` command.
-
-<a id="main.phen_publish"></a>
-
-#### phen\_publish
-
-```python
-def phen_publish(args: argparse.Namespace)
-```
-
-Handle the `phen publish` command.
-
-<a id="main.phen_copy"></a>
-
-#### phen\_copy
-
-```python
-def phen_copy(args: argparse.Namespace)
-```
-
-Handle the `phen copy` command.
-
-<a id="main.phen_diff"></a>
-
-#### phen\_diff
-
-```python
-def phen_diff(args: argparse.Namespace)
-```
-
-Handle the `phen diff` command.
-
-<a id="omop"></a>
-
-# omop
-
-OMOP Module
-================
-This module provides functionality to manage OMOP vocabularies.
-
-<a id="omop.install"></a>
-
-#### install
-
-```python
-def install(omop_zip_file: str, version: str)
-```
-
-Installs the OMOP release csv files in a file-based sql database
-
-<a id="omop.write_version_file"></a>
-
-#### write\_version\_file
-
-```python
-def write_version_file(version: str)
-```
-
-Writes the OMOP vocaburaries and version to a file
-
-<a id="omop.clear"></a>
-
-#### clear
-
-```python
-def clear(db_path: Path)
-```
-
-Clears the OMOP sql database
-
-<a id="omop.delete"></a>
-
-#### delete
-
-```python
-def delete(db_path: Path)
-```
-
-Deletes the OMOP sql database
-
-<a id="parse"></a>
-
-# parse
-
-<a id="parse.CodesError"></a>
-
-## CodesError Objects
-
-```python
-class CodesError()
-```
-
-A class used in InvalidCodesException to report an error if a code parser check fails
-
-<a id="parse.InvalidCodesException"></a>
-
-## InvalidCodesException Objects
-
-```python
-class InvalidCodesException(Exception)
-```
-
-Custom exception class raised when invalid codes are found that cannot be resolved by processing
-
-<a id="parse.Proto"></a>
-
-## Proto Objects
-
-```python
-class Proto()
-```
-
-Define checks as list of 3 tuple: (Message, Condition, Process)
-- Message = The name of the condition (what is printed and logged)
-- Condition = True if Passed, and False if Failed
-- Process = Aims to resolve all issues that stop condition from passing (Do not change index!)
-
-<a id="parse.Proto.raise_exception"></a>
-
-#### raise\_exception
-
-```python
-def raise_exception(ex: Exception)
-```
-
-Raises an exception inside a lambda function. Python does not allow using raise statement inside lambda because lambda can only contain expressions, not statements. Using raise_exception not raise_ as it's more explict
-
-<a id="parse.Proto.process"></a>
-
-#### process
-
-```python
-def process(codes: pd.DataFrame,
- codes_file: Path) -> Tuple[pd.DataFrame, list]
-```
-
-identify issues that do not pass and fix them with define/d process
-
-<a id="parse.Proto.verify"></a>
-
-#### verify
-
-```python
-def verify(codes: pd.DataFrame, codes_file: Path)
-```
-
-verify codes in codes file
-
-<a id="parse.Read2"></a>
-
-## Read2 Objects
-
-```python
-class Read2(Proto)
-```
-
-This Read2 class extends Proto, adding custom validation checks for a dataset of "Read2" codes. It ensures that the dataset is loaded, validates the codes based on several rules, and applies corrections or logs errors when necessary.
-
-<a id="parse.CodeTypeParser"></a>
-
-## CodeTypeParser Objects
-
-```python
-class CodeTypeParser()
-```
-
-A class used in InvalidCodesException to report an error if a code parser check fails
-
-<a id="phen"></a>
-
-# phen
-
-Phenotype Module
-================
-This module provides functionality for managing phenotypes.
-
-<a id="phen.PhenValidationException"></a>
-
-## PhenValidationException Objects
-
-```python
-class PhenValidationException(Exception)
-```
-
-Custom exception class raised when validation errors in phenotype configuration file
-
-<a id="phen.construct_git_url"></a>
-
-#### construct\_git\_url
-
-```python
-def construct_git_url(remote_url: str)
-```
-
-Constructs a git url for github or gitlab including a PAT token environment variable
-
-<a id="phen.create_empty_git_dir"></a>
-
-#### create\_empty\_git\_dir
-
-```python
-def create_empty_git_dir(path: Path)
-```
-
-Creates a directory with a .gitkeep file so that it's tracked in git
-
-<a id="phen.check_delete_dir"></a>
-
-#### check\_delete\_dir
-
-```python
-def check_delete_dir(path: Path, msg: str) -> bool
-```
-
-Checks on the command line if a user wants to delete a directory
-
-**Arguments**:
-
-- `path` _Path_ - path of the directory to be deleted
-- `msg` _str_ - message to be displayed to the user
-
-
-**Returns**:
-
-- `Boolean` - True if deleted
-
-<a id="phen.fork"></a>
-
-#### fork
-
-```python
-def fork(phen_dir: str, upstream_url: str, upstream_version: str,
- new_origin_url: str)
-```
-
-Forks an upstream phenotype in a remote repo at a specific version to a local director, and optionally sets to a new remote origin"
-
-**Arguments**:
-
-- `phen_dir` _str_ - local directory path where the upstream repo is to be cloned
-- `upstream_url` _str_ - url to the upstream repo
-- `upstream_version` _str_ - version in the upstream repo to clone
-- `new_origin_url` _str, optional_ - url of the remote repo to set as the new origin. Defaults to None.
-
-
-**Raises**:
-
-- `ValueError` - if the specified version is not in the upstream repo
-- `ValueError` - if the upstream repo is not a valid phenotype repo
-- `ValueError` - if there's any other problems with Git
-
-<a id="phen.init"></a>
-
-#### init
-
-```python
-def init(phen_dir: str, remote_url: str)
-```
-
-Initial phenotype directory as git repo with standard structure
-
-<a id="phen.validate"></a>
-
-#### validate
-
-```python
-def validate(phen_dir: str)
-```
-
-Validates the phenotype directory is a git repo with standard structure
-
-<a id="phen.read_table_file"></a>
-
-#### read\_table\_file
-
-```python
-def read_table_file(path: Path, excel_sheet: str = "")
-```
-
-Load Code List File
-
-<a id="phen.preprocess_source_concepts"></a>
-
-#### preprocess\_source\_concepts
-
-```python
-def preprocess_source_concepts(
- df: pd.DataFrame, concept_set: dict,
- code_file_path: Path) -> Tuple[pd.DataFrame, list]
-```
-
-Parses each column individually - Order and length will not be preserved!
-
-<a id="phen.translate_codes"></a>
-
-#### translate\_codes
-
-```python
-def translate_codes(source_df: pd.DataFrame, target_code_type: str,
- concept_name: str) -> pd.DataFrame
-```
-
-Translates each source code type the source coding list into a target type and returns all conversions as a concept set
-
-<a id="phen.publish"></a>
-
-#### publish
-
-```python
-def publish(phen_dir: str,
- msg: str,
- remote_url: str,
- increment: str = DEFAULT_VERSION_INC)
-```
-
-Publishes updates to the phenotype by commiting all changes to the repo directory
-
-<a id="phen.export"></a>
-
-#### export
-
-```python
-def export(phen_dir: str, version: str)
-```
-
-Exports a phen repo at a specific tagged version into a target directory
-
-<a id="phen.copy"></a>
-
-#### copy
-
-```python
-def copy(phen_dir: str, target_dir: str, version: str)
-```
-
-Copys a phen repo at a specific tagged version into a target directory
-
-<a id="phen.extract_concepts"></a>
-
-#### extract\_concepts
-
-```python
-def extract_concepts(config_data: dict) -> Tuple[dict, Set[str]]
-```
-
-Extracts concepts as {name: file_path} dictionary and a name set.
-
-<a id="phen.extract_clean_deepdiff_keys"></a>
-
-#### extract\_clean\_deepdiff\_keys
-
-```python
-def extract_clean_deepdiff_keys(diff: dict, key_type: str) -> Set[Any]
-```
-
-Extracts clean keys from a DeepDiff dictionary.
-
-**Arguments**:
-
-- `diff`: DeepDiff result dictionary
-- `key_type`: The type of change to extract (e.g., "dictionary_item_added", "dictionary_item_removed")
-
-**Returns**:
-
-A set of clean key names
-
-<a id="phen.diff_phen"></a>
-
-#### diff\_phen
-
-```python
-def diff_phen(new_phen_path: Path, new_version: str, old_phen_path: Path,
- old_version: str, report_path: Path)
-```
-
-Compare the differences between two versions of a phenotype
-
-<a id="trud"></a>
-
-# trud
-
-<a id="trud.get_releases"></a>
-
-#### get\_releases
-
-```python
-def get_releases(item_id: str, API_KEY: str, latest=False) -> list
-```
-
-Retrieve release information for an item from the TRUD API.
-
-<a id="trud.download_release_file"></a>
-
-#### download\_release\_file
-
-```python
-def download_release_file(item_id: str, release_ordinal: str, release: dict,
- file_json_prefix: str) -> Path
-```
-
-Download specified file type for a given release of an item.
-
-<a id="trud.create_map_directories"></a>
-
-#### create\_map\_directories
-
-```python
-def create_map_directories()
-```
-
-Create map directories.
-
diff --git a/docs/index.md b/docs/index.md
index ef5cc82be542d91f863ef52eb116feabbcc34cbe..0a6d9d81730213ad065f456c75642fe484cbceed 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -9,7 +9,7 @@
- [Example 1 - Basic local phenotype](./tutorials/example1.md)
- [Example 2 - More complex local phenotype](./tutorials/example2.md)
- [Example 3 - Using a remote git repository](./tutorials/example3.md)
- - [API Reference](./api.md)
+ - [API Reference](./api/acmc.html)
- [Change Log](./changelog.md)
- [Troubleshooting](./troubleshooting.md)
diff --git a/mkdocs.yml b/mkdocs.yml
index d2b555a075380b07bfbdb69dca3f85d3ecd1a23b..5a7d0497d1ac989a5abe3752e0c9a3971790cf9b 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -6,8 +6,16 @@ theme:
nav:
- Home: index.md
- - API:
- - acmc: api/acmc.html
+ - Installation: installation.md
+ - User Guide: user-guide.md
+ - Usage: usage.md
+ - Tutorial 1 Basic local phenotype: tutorials/example1.md
+ - Tutorial 2 More complex local phenotype: tutorials/example2.md
+ - Tutorial 3 Using a remote git repository: tutorials/example3.md
+ - API Reference:
+ - acmc: api/acmc.html
+ - Change Log: changelog.md
+ - Troubleshooting: troubleshooting.md
markdown_extensions:
- toc: