From 47d2a744c0d1adfdd18efa059720b2658fad12e8 Mon Sep 17 00:00:00 2001
From: Michal Stolarczyk <stolarczyk.michal93@gmail.com>
Date: Fri, 12 Mar 2021 14:57:36 -0500
Subject: [PATCH 1/9] use typing in pipestat.py

---
 docs/changelog.md    |   3 +
 pipestat/_version.py |   2 +-
 pipestat/pipestat.py | 201 +++++++++++++++++++++++++------------------
 3 files changed, 122 insertions(+), 84 deletions(-)

diff --git a/docs/changelog.md b/docs/changelog.md
index b01f3de0..3bd58c65 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -2,6 +2,9 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format. 
 
+## [0.0.4] - unreleased
+
+
 ## [0.0.3] - 2021-03-12
 ### Added
 - possibility to initialize the `PipestatManager` object (or use the `pipestat status` CLI) with no results schema defined for pipeline status management; [Issue #1](https://github.com/pepkit/pipestat/issues/1) 
diff --git a/pipestat/_version.py b/pipestat/_version.py
index 27fdca49..b288a61a 100644
--- a/pipestat/_version.py
+++ b/pipestat/_version.py
@@ -1 +1 @@
-__version__ = "0.0.3"
+__version__ = "0.0.4-dev"
diff --git a/pipestat/pipestat.py b/pipestat/pipestat.py
index 224c92ce..a6d1dfb6 100644
--- a/pipestat/pipestat.py
+++ b/pipestat/pipestat.py
@@ -1,6 +1,7 @@
 from contextlib import contextmanager
 from copy import deepcopy
 from logging import getLogger
+from typing import Any, Union, List, Dict, Optional
 
 import psycopg2
 from attmap import PathExAttMap as PXAM
@@ -48,14 +49,14 @@ class PipestatManager(dict):
 
     def __init__(
         self,
-        namespace=None,
-        record_identifier=None,
-        schema_path=None,
-        results_file_path=None,
-        database_only=False,
-        config=None,
-        status_schema_path=None,
-        flag_file_dir=None,
+        namespace: str = None,
+        record_identifier: str = None,
+        schema_path: str = None,
+        results_file_path: str = None,
+        database_only: bool = False,
+        config: Union[str, dict] = None,
+        status_schema_path: str = None,
+        flag_file_dir: str = None,
     ):
         """
         Initialize the object
@@ -77,16 +78,19 @@ def __init__(
             the status flags structure
         """
 
-        def _check_cfg_key(cfg, key):
+        def _check_cfg_key(cfg: dict, key: str) -> bool:
             if key not in cfg:
                 _LOGGER.warning(f"Key '{key}' not found in config")
                 return False
             return True
 
-        def _mk_abs_via_cfg(path, cfg_path):
+        def _mk_abs_via_cfg(
+            path: Optional[str],
+            cfg_path: Optional[str],
+        ) -> Optional[str]:
             if path is None:
-                return
-            path = expandpath(path)
+                return path
+            assert isinstance(path, str), "Path is expected to be a str"
             if os.path.isabs(path):
                 return path
             if cfg_path is None:
@@ -99,7 +103,13 @@ def _mk_abs_via_cfg(path, cfg_path):
                 return joined
             raise OSError(f"Could not make this path absolute: {path}")
 
-        def _select_value(arg_name, arg_value, cfg, strict=True, env_var=None):
+        def _select_value(
+            arg_name: str,
+            arg_value: Any,
+            cfg: dict,
+            strict: bool = True,
+            env_var: str = None,
+        ) -> Any:
             if arg_value is not None:
                 return arg_value
             if arg_name not in cfg or cfg[arg_name] is None:
@@ -128,6 +138,7 @@ def _select_value(arg_name, arg_value, cfg, strict=True, env_var=None):
                 self._config_path = config
             elif isinstance(config, dict):
                 self[CONFIG_KEY] = YacAttMap(entries=config)
+                self._config_path = None
             else:
                 raise TypeError(
                     "database_config has to be either path to the "
@@ -160,17 +171,14 @@ def _select_value(arg_name, arg_value, cfg, strict=True, env_var=None):
         )
         if self._schema_path is not None:
             _, self[SCHEMA_KEY] = read_yaml_data(
-                _mk_abs_via_cfg(self._schema_path, config), "schema"
+                _mk_abs_via_cfg(self._schema_path, self.config_path), "schema"
             )
             self.validate_schema()
             # determine the highlighted results
-            # the conditional in the list comprehension below needs to be a
-            # literal "== True" so that if evaluates to False if 'highlight'
-            # value is just "truthy", not True
             self[HIGHLIGHTED_KEY] = [
                 k
                 for k, v in self.schema.items()
-                if "highlight" in v and v["highlight"] == True
+                if "highlight" in v and v["highlight"] is True
             ]
             if self[HIGHLIGHTED_KEY]:
                 assert isinstance(self[HIGHLIGHTED_KEY], list), TypeError(
@@ -187,7 +195,7 @@ def _select_value(arg_name, arg_value, cfg, strict=True, env_var=None):
                     False,
                     env_var=ENV_VARS["status_schema"],
                 ),
-                config,
+                self.config_path,
             )
             or STATUS_SCHEMA
         )
@@ -203,7 +211,7 @@ def _select_value(arg_name, arg_value, cfg, strict=True, env_var=None):
                 False,
                 ENV_VARS["results_file"],
             ),
-            config,
+            self.config_path,
         )
         if results_file_path:
             if self[DB_ONLY_KEY]:
@@ -252,12 +260,14 @@ def __str__(self):
             res += f"\nHighlighted results: {', '.join(self.highlighted_results)}"
         return res
 
-    def _get_flag_file(self, record_identifier=None):
+    def _get_flag_file(
+        self, record_identifier: str = None
+    ) -> Union[str, List[str], None]:
         """
         Get path to the status flag file for the specified record
 
         :param str record_identifier: unique record identifier
-        :return str: path to the status flag file
+        :return str | list[str] | None: path to the status flag file
         """
         from glob import glob
 
@@ -276,19 +286,19 @@ def _get_flag_file(self, record_identifier=None):
                 return file_list[0]
             else:
                 _LOGGER.debug("No flag files found")
-                return
+                return None
 
     @property
-    def highlighted_results(self):
+    def highlighted_results(self) -> List[str]:
         """
         Highlighted results
 
-        :return list[str]: a collection of highlighted results
+        :return List[str]: a collection of highlighted results
         """
         return self._get_attr(HIGHLIGHTED_KEY) or []
 
     @property
-    def record_count(self):
+    def record_count(self) -> int:
         """
         Number of records reported
 
@@ -301,7 +311,7 @@ def record_count(self):
         )
 
     @property
-    def namespace(self):
+    def namespace(self) -> str:
         """
         Namespace the object writes the results to
 
@@ -310,7 +320,7 @@ def namespace(self):
         return self._get_attr(NAME_KEY)
 
     @property
-    def record_identifier(self):
+    def record_identifier(self) -> str:
         """
         Unique identifier of the record
 
@@ -319,7 +329,7 @@ def record_identifier(self):
         return self._get_attr(RECORD_ID_KEY)
 
     @property
-    def schema(self):
+    def schema(self) -> Dict:
         """
         Schema mapping
 
@@ -328,7 +338,7 @@ def schema(self):
         return self._get_attr(SCHEMA_KEY)
 
     @property
-    def status_schema(self):
+    def status_schema(self) -> Dict:
         """
         Status schema mapping
 
@@ -337,7 +347,7 @@ def status_schema(self):
         return self._get_attr(STATUS_SCHEMA_KEY)
 
     @property
-    def status_schema_source(self):
+    def status_schema_source(self) -> Dict:
         """
         Status schema source
 
@@ -347,7 +357,7 @@ def status_schema_source(self):
         return self._get_attr(STATUS_SCHEMA_SOURCE_KEY)
 
     @property
-    def schema_path(self):
+    def schema_path(self) -> str:
         """
         Schema path
 
@@ -356,7 +366,7 @@ def schema_path(self):
         return self._schema_path
 
     @property
-    def config_path(self):
+    def config_path(self) -> str:
         """
         Config path. None if the config was not provided or if provided
         as a mapping of the config contents
@@ -366,7 +376,7 @@ def config_path(self):
         return getattr(self, "_config_path", None)
 
     @property
-    def result_schemas(self):
+    def result_schemas(self) -> Dict:
         """
         Result schema mappings
 
@@ -376,7 +386,7 @@ def result_schemas(self):
         return self._get_attr(RES_SCHEMAS_KEY)
 
     @property
-    def file(self):
+    def file(self) -> str:
         """
         File path that the object is reporting the results into
 
@@ -385,7 +395,7 @@ def file(self):
         return self._get_attr(FILE_KEY)
 
     @property
-    def data(self):
+    def data(self) -> YacAttMap:
         """
         Data object
 
@@ -393,8 +403,8 @@ def data(self):
         """
         return self._get_attr(DATA_KEY)
 
-    @property
     @contextmanager
+    @property
     def db_cursor(self):
         """
         Establish connection and get a PostgreSQL database cursor,
@@ -414,7 +424,7 @@ def db_cursor(self):
         finally:
             self.close_postgres_connection()
 
-    def get_status(self, record_identifier=None):
+    def get_status(self, record_identifier: str = None) -> Optional[str]:
         """
         Get the current pipeline status
 
@@ -434,6 +444,9 @@ def get_status(self, record_identifier=None):
         else:
             flag_file = self._get_flag_file(record_identifier=r_id)
             if flag_file is not None:
+                assert isinstance(
+                    flag_file, str
+                ), "Flag file path is expected to be a str, were multiple flags found?"
                 with open(flag_file, "r") as f:
                     status = f.read()
                 return status
@@ -441,9 +454,9 @@ def get_status(self, record_identifier=None):
                 f"Could not determine status for '{r_id}' record. "
                 f"No flags found in: {self[STATUS_FILE_DIR]}"
             )
-            return
+            return None
 
-    def _get_attr(self, attr):
+    def _get_attr(self, attr: str) -> Any:
         """
         Safely get the name of the selected attribute of this object
 
@@ -452,11 +465,9 @@ def _get_attr(self, attr):
         """
         return self[attr] if attr in self else None
 
-    def _table_to_dict(self):
+    def _table_to_dict(self) -> None:
         """
         Create a dictionary from the database table data
-
-        :return dict: database table data in a dict form
         """
         with self.db_cursor as cur:
             cur.execute(f"SELECT * FROM {self.namespace}")
@@ -470,7 +481,7 @@ def _table_to_dict(self):
                         record_identifier=record_id, values={res_id: val}
                     )
 
-    def _init_postgres_table(self):
+    def _init_postgres_table(self) -> bool:
         """
         Initialize a PostgreSQL table based on the provided schema,
         if it does not exist. Read the data stored in the database into the
@@ -511,12 +522,12 @@ def _init_status_table(self):
             )
             self._create_table(status_table_name, STATUS_TABLE_COLUMNS)
 
-    def _create_table(self, table_name, columns):
+    def _create_table(self, table_name: str, columns: List[str]):
         """
         Create a table
 
         :param str table_name: name of the table to create
-        :param str | list[str] columns: columns definition list,
+        :param str | List[str] columns: columns definition list,
             for instance: ['name VARCHAR(50) NOT NULL']
         """
         columns = mk_list_of_str(columns)
@@ -524,7 +535,7 @@ def _create_table(self, table_name, columns):
             s = sql.SQL(f"CREATE TABLE {table_name} ({','.join(columns)})")
             cur.execute(s)
 
-    def _init_results_file(self):
+    def _init_results_file(self) -> bool:
         """
         Initialize YAML results file if it does not exist.
         Read the data stored in the existing file into the memory otherwise.
@@ -549,7 +560,7 @@ def _init_results_file(self):
         self[DATA_KEY] = data
         return False
 
-    def _check_table_exists(self, table_name):
+    def _check_table_exists(self, table_name: str) -> bool:
         """
         Check if the specified table exists
 
@@ -564,12 +575,15 @@ def _check_table_exists(self, table_name):
             )
             return cur.fetchone()[0]
 
-    def _check_record(self, condition_col, condition_val, table_name):
+    def _check_record(
+        self, condition_col: str, condition_val: str, table_name: str
+    ) -> bool:
         """
         Check if the record matching the condition is in the table
 
         :param str condition_col: column to base the check on
         :param str condition_val: value in the selected column
+        :param str table_name: name of the table ot check the record in
         :return bool: whether any record matches the provided condition
         """
         with self.db_cursor as cur:
@@ -580,7 +594,7 @@ def _check_record(self, condition_col, condition_val, table_name):
             cur.execute(statement, (condition_val,))
             return cur.fetchone()[0]
 
-    def _count_rows(self, table_name):
+    def _count_rows(self, table_name: str) -> int:
         """
         Count rows in a selected table
 
@@ -594,7 +608,9 @@ def _count_rows(self, table_name):
             cur.execute(statement)
             return cur.fetchall()[0][0]
 
-    def _report_postgres(self, value, record_identifier, table_name=None):
+    def _report_postgres(
+        self, value: Dict[str, Any], record_identifier: str, table_name: str = None
+    ) -> int:
         """
         Check if record with this record identifier in table, create new record
          if not (INSERT), update the record if yes (UPDATE).
@@ -638,14 +654,16 @@ def _report_postgres(self, value, record_identifier, table_name=None):
             cur.execute(query, values)
             return cur.fetchone()[0]
 
-    def clear_status(self, record_identifier=None, flag_names=None):
+    def clear_status(
+        self, record_identifier: str = None, flag_names: List[str] = None
+    ) -> List[str]:
         """
         Remove status flags
 
         :param str record_identifier: name of the record to remove flags for
         :param Iterable[str] flag_names: Names of flags to remove, optional; if
             unspecified, all schema-defined flag names will be used.
-        :return list[str]: Collection of names of flags removed
+        :return List[str]: Collection of names of flags removed
         """
         r_id = self._strict_record_id(record_identifier)
         if self.file is not None:
@@ -683,7 +701,9 @@ def clear_status(self, record_identifier=None, flag_names=None):
                 else:
                     return [removed]
 
-    def get_status_flag_path(self, status_identifier, record_identifier=None):
+    def get_status_flag_path(
+        self, status_identifier: str, record_identifier=None
+    ) -> str:
         """
         Get the path to the status file flag
 
@@ -701,7 +721,7 @@ def get_status_flag_path(self, status_identifier, record_identifier=None):
             self[STATUS_FILE_DIR], f"{self.namespace}_{r_id}_{status_identifier}.flag"
         )
 
-    def set_status(self, status_identifier, record_identifier=None):
+    def set_status(self, status_identifier: str, record_identifier: str = None) -> None:
         """
         Set pipeline run status.
 
@@ -762,13 +782,15 @@ def check_result_exists(self, result_identifier, record_identifier=None):
             results=[result_identifier], rid=record_identifier
         )
 
-    def _check_which_results_exist(self, results, rid=None):
+    def _check_which_results_exist(
+        self, results: List[str], rid: str = None
+    ) -> List[str]:
         """
         Check which results have been reported
 
         :param str rid: unique identifier of the record
-        :param list[str] results: names of the results to check
-        :return bool: whether the specified result has been reported for the
+        :param List[str] results: names of the results to check
+        :return List[str]: whether the specified result has been reported for the
             indicated record in current namespace
         """
         rid = self._strict_record_id(rid)
@@ -796,7 +818,7 @@ def _check_which_results_exist(self, results, rid=None):
                             existing.append(r)
         return existing
 
-    def check_record_exists(self, record_identifier=None):
+    def check_record_exists(self, record_identifier: str = None) -> bool:
         """
         Check if the record exists
 
@@ -821,16 +843,16 @@ def check_record_exists(self, record_identifier=None):
 
     def report(
         self,
-        values,
-        record_identifier=None,
-        force_overwrite=False,
-        strict_type=True,
-        return_id=False,
-    ):
+        values: Dict[str, Any],
+        record_identifier: str = None,
+        force_overwrite: bool = False,
+        strict_type: bool = True,
+        return_id: bool = False,
+    ) -> Union[bool, int]:
         """
         Report a result.
 
-        :param dict[str, any] values: dictionary of result-value pairs
+        :param Dict[str, any] values: dictionary of result-value pairs
         :param str record_identifier: unique identifier of the record, value
             in 'record_identifier' column to look for to determine if the record
             already exists
@@ -849,6 +871,7 @@ def report(
                 "There is no way to return the updated object ID while using "
                 "results file as the object backend"
             )
+        updated_ids = False
         if self.schema is None:
             raise SchemaNotFoundError("report results")
         result_identifiers = list(values.keys())
@@ -897,7 +920,9 @@ def report(
         )
         return True if not return_id else updated_ids
 
-    def _report_data_element(self, record_identifier, values):
+    def _report_data_element(
+        self, record_identifier: str, values: Dict[str, Any]
+    ) -> None:
         """
         Update the value of a result in a current namespace.
 
@@ -905,7 +930,8 @@ def _report_data_element(self, record_identifier, values):
          hierarchical mapping structure if needed.
 
         :param str record_identifier: unique identifier of the record
-        :param any values: dict of results identifiers and values to be reported
+        :param Dict[str,Any] values: dict of results identifiers and values
+            to be reported
         """
         self[DATA_KEY].setdefault(self.namespace, PXAM())
         self[DATA_KEY][self.namespace].setdefault(record_identifier, PXAM())
@@ -913,13 +939,18 @@ def _report_data_element(self, record_identifier, values):
             self[DATA_KEY][self.namespace][record_identifier][res_id] = val
 
     def select(
-        self, columns=None, condition=None, condition_val=None, offset=None, limit=None
-    ):
+        self,
+        columns: Union[str, List[str]] = None,
+        condition: str = None,
+        condition_val: str = None,
+        offset: int = None,
+        limit: int = None,
+    ) -> List[psycopg2.extras.DictRow]:
         """
         Get all the contents from the selected table, possibly restricted by
         the provided condition.
 
-        :param str | list[str] columns: columns to select
+        :param str | List[str] columns: columns to select
         :param str condition: condition to restrict the results
             with, will be appended to the end of the SELECT statement and
             safely populated with 'condition_val',
@@ -928,7 +959,7 @@ def select(
             in 'condition' with
         :param int offset: number of records to be skipped
         :param int limit: max number of records to be returned
-        :return list[psycopg2.extras.DictRow]: all table contents
+        :return List[psycopg2.extras.DictRow]: all table contents
         """
         if self.file:
             raise NotImplementedError(
@@ -954,7 +985,9 @@ def select(
             result = cur.fetchall()
         return result
 
-    def retrieve(self, record_identifier=None, result_identifier=None):
+    def retrieve(
+        self, record_identifier: str = None, result_identifier: str = None
+    ) -> Union[Any, Dict[str, Any]]:
         """
         Retrieve a result for a record.
 
@@ -963,7 +996,7 @@ def retrieve(self, record_identifier=None, result_identifier=None):
 
         :param str record_identifier: unique identifier of the record
         :param str result_identifier: name of the result to be retrieved
-        :return any | dict[str, any]: a single result or a mapping with all the
+        :return any | Dict[str, any]: a single result or a mapping with all the
             results reported for the record
         """
         record_identifier = self._strict_record_id(record_identifier)
@@ -1001,7 +1034,9 @@ def retrieve(self, record_identifier=None, result_identifier=None):
                 )
             return self.data[self.namespace][record_identifier][result_identifier]
 
-    def remove(self, record_identifier=None, result_identifier=None):
+    def remove(
+        self, record_identifier: str = None, result_identifier: str = None
+    ) -> bool:
         """
         Remove a result.
 
@@ -1084,14 +1119,14 @@ def remove(self, record_identifier=None, result_identifier=None):
                 raise
         return True
 
-    def validate_schema(self):
+    def validate_schema(self) -> None:
         """
         Check schema for any possible issues
 
         :raises SchemaError: if any schema format issue is detected
         """
 
-        def _recursively_replace_custom_types(s):
+        def _recursively_replace_custom_types(s: dict) -> Dict:
             """
             Replace the custom types in pipestat schema with canonical types
 
@@ -1132,11 +1167,11 @@ def _recursively_replace_custom_types(s):
         schema = _recursively_replace_custom_types(schema)
         self[RES_SCHEMAS_KEY] = schema
 
-    def assert_results_defined(self, results):
+    def assert_results_defined(self, results: List[str]) -> None:
         """
         Assert provided list of results is defined in the schema
 
-        :param list[str] results: list of results to
+        :param List[str] results: list of results to
             check for existence in the schema
         :raises SchemaError: if any of the results is not defined in the schema
         """
@@ -1147,7 +1182,7 @@ def assert_results_defined(self, results):
                 f"schema are: {list(known_results)}."
             )
 
-    def check_connection(self):
+    def check_connection(self) -> bool:
         """
         Check whether a PostgreSQL connection has been established
 
@@ -1163,7 +1198,7 @@ def check_connection(self):
             return True
         return False
 
-    def establish_postgres_connection(self, suppress=False):
+    def establish_postgres_connection(self, suppress: bool = False) -> bool:
         """
         Establish PostgreSQL connection using the config data
 
@@ -1199,7 +1234,7 @@ def establish_postgres_connection(self, suppress=False):
             )
             return True
 
-    def close_postgres_connection(self):
+    def close_postgres_connection(self) -> None:
         """
         Close connection and remove client bound
         """
@@ -1215,7 +1250,7 @@ def close_postgres_connection(self):
             f"{self[CONFIG_KEY][CFG_DATABASE_KEY][CFG_HOST_KEY]}"
         )
 
-    def _strict_record_id(self, forced_value=None):
+    def _strict_record_id(self, forced_value: str = None) -> str:
         """
         Get record identifier from the outer source or stored with this object
 

From 0ee23f1f547c8d984b12b594d68312f9db66939a Mon Sep 17 00:00:00 2001
From: Michal Stolarczyk <stolarczyk.michal93@gmail.com>
Date: Fri, 12 Mar 2021 15:01:02 -0500
Subject: [PATCH 2/9] switch decorators

---
 pipestat/pipestat.py | 2 +-
 setup.py             | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/pipestat/pipestat.py b/pipestat/pipestat.py
index a6d1dfb6..ca83ebb4 100644
--- a/pipestat/pipestat.py
+++ b/pipestat/pipestat.py
@@ -403,8 +403,8 @@ def data(self) -> YacAttMap:
         """
         return self._get_attr(DATA_KEY)
 
-    @contextmanager
     @property
+    @contextmanager
     def db_cursor(self):
         """
         Establish connection and get a PostgreSQL database cursor,
diff --git a/setup.py b/setup.py
index d7e92fa8..5b437d28 100644
--- a/setup.py
+++ b/setup.py
@@ -68,6 +68,7 @@ def get_static(name, condition=None):
         "Programming Language :: Python :: 3.6",
         "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
     ],
     keywords="project, metadata, bioinformatics, sequencing, ngs, workflow",

From ebc7dafb9cdb07f74138096ae472d7805945e9b9 Mon Sep 17 00:00:00 2001
From: Michal Stolarczyk <stolarczyk.michal93@gmail.com>
Date: Fri, 12 Mar 2021 15:03:46 -0500
Subject: [PATCH 3/9] change exception type

---
 pipestat/pipestat.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/pipestat/pipestat.py b/pipestat/pipestat.py
index ca83ebb4..497d1a10 100644
--- a/pipestat/pipestat.py
+++ b/pipestat/pipestat.py
@@ -90,7 +90,7 @@ def _mk_abs_via_cfg(
         ) -> Optional[str]:
             if path is None:
                 return path
-            assert isinstance(path, str), "Path is expected to be a str"
+            assert isinstance(path, str), TypeError("Path is expected to be a str")
             if os.path.isabs(path):
                 return path
             if cfg_path is None:
@@ -444,9 +444,9 @@ def get_status(self, record_identifier: str = None) -> Optional[str]:
         else:
             flag_file = self._get_flag_file(record_identifier=r_id)
             if flag_file is not None:
-                assert isinstance(
-                    flag_file, str
-                ), "Flag file path is expected to be a str, were multiple flags found?"
+                assert isinstance(flag_file, str), TypeError(
+                    "Flag file path is expected to be a str, were multiple flags found?"
+                )
                 with open(flag_file, "r") as f:
                     status = f.read()
                 return status

From 6431240e72b5e21a1f6f687d681095e5d5c738ca Mon Sep 17 00:00:00 2001
From: Michal Stolarczyk <stolarczyk.michal93@gmail.com>
Date: Fri, 12 Mar 2021 15:10:33 -0500
Subject: [PATCH 4/9] expect assertionerror

---
 tests/test_pipestat.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_pipestat.py b/tests/test_pipestat.py
index 2a2907f5..b8eef8df 100644
--- a/tests/test_pipestat.py
+++ b/tests/test_pipestat.py
@@ -186,7 +186,7 @@ def test_use_other_namespace_file(self, schema_file_path):
     @pytest.mark.parametrize("pth", [["/$HOME/path.yaml"], 1])
     def test_wrong_class_results_file(self, schema_file_path, pth):
         """ Input string that is not a file path raises an informative error """
-        with pytest.raises(TypeError):
+        with pytest.raises((TypeError, AssertionError)):
             PipestatManager(
                 namespace="test", results_file_path=pth, schema_path=schema_file_path
             )

From e33539d88bd44269410d757d9009d96b7be1ff4c Mon Sep 17 00:00:00 2001
From: Michal Stolarczyk <stolarczyk.michal93@gmail.com>
Date: Mon, 15 Mar 2021 10:00:41 -0400
Subject: [PATCH 5/9] add pre-commit cfg

---
 .pre-commit-config.yaml           | 21 +++++++++++++++++++++
 requirements/requirements-dev.txt |  1 +
 2 files changed, 22 insertions(+)
 create mode 100644 .pre-commit-config.yaml

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 00000000..16cccb97
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,21 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.4.0
+    hooks:
+      - id: trailing-whitespace
+      - id: check-yaml
+      - id: check-json
+      - id: end-of-file-fixer
+      - id: name-tests-test
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/psf/black
+    rev: 20.8b1
+    hooks:
+      - id: black
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.7.0
+    hooks:
+      - id: isort
diff --git a/requirements/requirements-dev.txt b/requirements/requirements-dev.txt
index e69de29b..416634f5 100644
--- a/requirements/requirements-dev.txt
+++ b/requirements/requirements-dev.txt
@@ -0,0 +1 @@
+pre-commit

From 7d60f79081a92ca190f6be0653091fea704af58c Mon Sep 17 00:00:00 2001
From: Michal Stolarczyk <stolarczyk.michal93@gmail.com>
Date: Tue, 16 Mar 2021 15:39:34 -0400
Subject: [PATCH 6/9] account for nonexistent path, but check if writable

---
 .gitignore           | 3 ++-
 pipestat/pipestat.py | 6 ++++--
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/.gitignore b/.gitignore
index a2f7f89d..fcf0f3c8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,6 +6,7 @@
 __pycache__
 *.py[cod]
 *$py.class
+__pycache__/
 
 # C extensions
 *.so
@@ -131,4 +132,4 @@ venv.bak/
 dmypy.json
 
 # Pyre type checker
-.pyre/
\ No newline at end of file
+.pyre/
diff --git a/pipestat/pipestat.py b/pipestat/pipestat.py
index 497d1a10..1cb27eb5 100644
--- a/pipestat/pipestat.py
+++ b/pipestat/pipestat.py
@@ -1,7 +1,7 @@
 from contextlib import contextmanager
 from copy import deepcopy
 from logging import getLogger
-from typing import Any, Union, List, Dict, Optional
+from typing import Any, Dict, List, Optional, Union
 
 import psycopg2
 from attmap import PathExAttMap as PXAM
@@ -95,7 +95,9 @@ def _mk_abs_via_cfg(
                 return path
             if cfg_path is None:
                 rel_to_cwd = os.path.join(os.getcwd(), path)
-                if os.path.exists(rel_to_cwd):
+                if os.path.exists(rel_to_cwd) or os.access(
+                    os.path.dirname(rel_to_cwd), os.W_OK
+                ):
                     return rel_to_cwd
                 raise OSError(f"Could not make this path absolute: {path}")
             joined = os.path.join(os.path.dirname(cfg_path), path)

From e96ddedb0cd7219720aaf433c5330de52c53eff6 Mon Sep 17 00:00:00 2001
From: Michal Stolarczyk <stolarczyk.michal93@gmail.com>
Date: Tue, 16 Mar 2021 15:50:49 -0400
Subject: [PATCH 7/9] add config validation, update yacman req

---
 pipestat/pipestat.py              | 8 ++++----
 requirements/requirements-all.txt | 8 ++++----
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/pipestat/pipestat.py b/pipestat/pipestat.py
index 1cb27eb5..f3f75262 100644
--- a/pipestat/pipestat.py
+++ b/pipestat/pipestat.py
@@ -5,6 +5,7 @@
 
 import psycopg2
 from attmap import PathExAttMap as PXAM
+from jsonschema import validate
 from psycopg2.extensions import connection
 from psycopg2.extras import DictCursor, Json
 from ubiquerg import create_lock, remove_lock
@@ -147,10 +148,9 @@ def _select_value(
                     "file to read or a dict"
                 )
             # validate config
-            # TODO: uncomment below when this gets released: https://github.com/pepkit/attmap/pull/75
-            # cfg = self[CONFIG_KEY].to_dict(expand=True)
-            # _, cfg_schema = read_yaml_data(CFG_SCHEMA, "config schema")
-            # validate(cfg, cfg_schema)
+            cfg = self[CONFIG_KEY].to_dict(expand=True)
+            _, cfg_schema = read_yaml_data(CFG_SCHEMA, "config schema")
+            validate(cfg, cfg_schema)
 
         self[NAME_KEY] = _select_value(
             "namespace", namespace, self[CONFIG_KEY], env_var=ENV_VARS["namespace"]
diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt
index 406e4ad8..e0d427df 100644
--- a/requirements/requirements-all.txt
+++ b/requirements/requirements-all.txt
@@ -1,7 +1,7 @@
-ubiquerg>=0.6.1
+attmap
+jsonschema
 logmuse>=0.2.5
 oyaml
-yacman>=0.7.0
 psycopg2-binary
-attmap
-jsonschema
\ No newline at end of file
+ubiquerg>=0.6.1
+yacman>=0.8.0

From 8dd368dc8ca8bd1f81cb7a610c066d7022624ce6 Mon Sep 17 00:00:00 2001
From: Michal Stolarczyk <stolarczyk.michal93@gmail.com>
Date: Fri, 2 Apr 2021 07:13:00 -0400
Subject: [PATCH 8/9] temporary black fix;
 https://github.com/psf/black/issues/2079

---
 .github/workflows/black.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml
index f58e4c63..63e18519 100644
--- a/.github/workflows/black.yml
+++ b/.github/workflows/black.yml
@@ -8,4 +8,4 @@ jobs:
     steps:
       - uses: actions/checkout@v2
       - uses: actions/setup-python@v2
-      - uses: psf/black@stable
+      - uses: psf/black@20.8b1

From 532fcff49a11cf61662a82d5a4ffb5bd7550f25c Mon Sep 17 00:00:00 2001
From: Michal Stolarczyk <stolarczyk.michal93@gmail.com>
Date: Fri, 2 Apr 2021 07:18:40 -0400
Subject: [PATCH 9/9] prep release

---
 docs/changelog.md    | 11 +++++++----
 pipestat/_version.py |  2 +-
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/docs/changelog.md b/docs/changelog.md
index 3bd58c65..8419336f 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -1,15 +1,18 @@
 # Changelog
 
-This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format. 
+This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
-## [0.0.4] - unreleased
+## [0.0.4] - 2021-04-02
+### Added
+- config validation
+- typing in code
 
 
 ## [0.0.3] - 2021-03-12
 ### Added
-- possibility to initialize the `PipestatManager` object (or use the `pipestat status` CLI) with no results schema defined for pipeline status management; [Issue #1](https://github.com/pepkit/pipestat/issues/1) 
+- possibility to initialize the `PipestatManager` object (or use the `pipestat status` CLI) with no results schema defined for pipeline status management; [Issue #1](https://github.com/pepkit/pipestat/issues/1)
 
 
 ## [0.0.2] - 2021-02-22
 ### Added
-- initial package release
\ No newline at end of file
+- initial package release
diff --git a/pipestat/_version.py b/pipestat/_version.py
index b288a61a..81f0fdec 100644
--- a/pipestat/_version.py
+++ b/pipestat/_version.py
@@ -1 +1 @@
-__version__ = "0.0.4-dev"
+__version__ = "0.0.4"