From 26ab13f7df8d481ccf38c751edfda3eb4e922d3f Mon Sep 17 00:00:00 2001
From: Bryant Chow <bryant.h.c@gmail.com>
Date: Thu, 8 Dec 2022 11:46:19 -0900
Subject: [PATCH 1/2] replaced old-school setup.py with new-school
 pyproject.toml file, removed ununsed environment.yaml file which may be
 replaced later when Conda install is attempted

---
 environment.yml |  7 -------
 pyproject.toml  | 39 +++++++++++++++++++++++++++++++++++++++
 setup.py        | 25 -------------------------
 3 files changed, 39 insertions(+), 32 deletions(-)
 delete mode 100644 environment.yml
 create mode 100644 pyproject.toml
 delete mode 100644 setup.py

diff --git a/environment.yml b/environment.yml
deleted file mode 100644
index 51de15c..0000000
--- a/environment.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-name: pysep
-channels:
-  - conda-forge
-  - defaults
-dependencies:
-  - obspy
-  - cartopy
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..700fadb
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,39 @@
+[build-system]
+requires = ["setuptools>=61.0.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "PySEP"
+description = "Python Seismogram Extraction and Processing"
+readme = "README.md"
+requires-python = ">=3.7"
+license = "MIT"
+version = "0.2.0"
+authors = [
+    {name = "adjTomo Dev Team"},
+    {email = "adjtomo@gmail.com"}
+]
+maintainers = [
+    {name = "Bryant Chow",
+     email = "bhchow@alaska.edu"}
+]
+dependencies = [
+    "obspy",
+    "cartopy",
+    "pyyaml",
+    "llnl_db_client @ git+https://github.com/krischer/llnl_db_client.git"
+]
+
+[project.optional-dependencies]
+test = [
+    "pytest",
+]
+
+[project.urls]
+homepage = "https://github.com/adjtomo/"
+documentation = "https://github.com/adjtomo/pysep/wiki"
+repository = "https://github.com/adjtomo/pysep"
+
+[project.scripts]
+pysep = "pysep.pysep:main"
+recsec = "pysep.recsec.main"
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 7a73e7d..0000000
--- a/setup.py
+++ /dev/null
@@ -1,25 +0,0 @@
-import os
-from setuptools import setup, find_packages
-
-
-install_requires = [
-        "obspy>=1.2.2", 
-        "cartopy>=0.20.2", 
-        "pyyaml>=5.4",
-        "llnl_db_client @ git+https://github.com/krischer/llnl_db_client.git",
-        ]
-
-setup(name="pysep",
-      version='0.2.0',
-      description="Python Seismogram Extraction and Processing",
-      url="http://github.com/adjtomo/pysep",
-      author='adjTomo Dev Team',
-      license='GPL-3.0',
-      python_requires=">=3.7",
-      packages=find_packages(),
-      install_requires=install_requires,
-      entry_points={"console_scripts": ["pysep=pysep.pysep:main",
-                                        "recsec=pysep.recsec:main"]
-                                        },
-      zip_safe=False
-      )

From 83d8bd98389005f35ecff03b0c581c181751a6df Mon Sep 17 00:00:00 2001
From: Bryant Chow <bryant.h.c@gmail.com>
Date: Thu, 8 Dec 2022 12:23:16 -0900
Subject: [PATCH 2/2] direct pip install will not work due to some dependency
 errors with cartopy and GEOS but .toml file still valid. added conda-required
 environment.yaml file which will be used to do the entire install procedure

---
 environment.yml  | 13 +++++++++++++
 pyproject.toml   | 17 ++++++-----------
 pysep/recsec.py  |  2 +-
 requirements.txt |  5 -----
 4 files changed, 20 insertions(+), 17 deletions(-)
 create mode 100644 environment.yml
 delete mode 100644 requirements.txt

diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..c8d4f9e
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,13 @@
+name: pysep
+channels:
+    - conda-forge
+    - defaults
+dependencies:
+    - pip
+    - obspy
+    - cartopy
+    - pyyaml
+    - pip:
+      - git+https://github.com/krischer/llnl_db_client.git
+      - -e .
+       
diff --git a/pyproject.toml b/pyproject.toml
index 700fadb..b6e7f10 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -3,20 +3,16 @@ requires = ["setuptools>=61.0.0", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "PySEP"
+name = "pysep"
+version = "0.2.0"
 description = "Python Seismogram Extraction and Processing"
 readme = "README.md"
 requires-python = ">=3.7"
-license = "MIT"
-version = "0.2.0"
+license = {file = "LICENSE.txt"}
 authors = [
     {name = "adjTomo Dev Team"},
     {email = "adjtomo@gmail.com"}
 ]
-maintainers = [
-    {name = "Bryant Chow",
-     email = "bhchow@alaska.edu"}
-]
 dependencies = [
     "obspy",
     "cartopy",
@@ -25,9 +21,8 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-test = [
-    "pytest",
-]
+test = ["pytest"]
+dev = ["pytest", "ipython", "ipdb"]
 
 [project.urls]
 homepage = "https://github.com/adjtomo/"
@@ -36,4 +31,4 @@ repository = "https://github.com/adjtomo/pysep"
 
 [project.scripts]
 pysep = "pysep.pysep:main"
-recsec = "pysep.recsec.main"
+recsec = "pysep.recsec:main"
diff --git a/pysep/recsec.py b/pysep/recsec.py
index a5ff5b5..bef2a11 100755
--- a/pysep/recsec.py
+++ b/pysep/recsec.py
@@ -1887,7 +1887,7 @@ def parse_args():
     """
     parser = argparse.ArgumentParser(
         description="Input basic record section params",
-        formatter_class=argparse.RawTextHelpFormatter,
+        # formatter_class=argparse.RawTextHelpFormatter,
                                      )
 
     parser.add_argument("-p", "--pysep_path", default="./", type=str, nargs="?",
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index 3723eca..0000000
--- a/requirements.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-obspy>=1.2.2
-pyyaml>=5.4
-cartopy>=0.20.2
-pytest>=7.1.2
-pandas>=1.4.2