From e671fcfff8f8565deba18c10b3cd36e06fa99988 Mon Sep 17 00:00:00 2001
From: Joseph D Hughes <jdhughes@usgs.gov>
Date: Thu, 15 Feb 2024 11:28:08 -0600
Subject: [PATCH 1/2] refactor(pymake): limit targets added to zip files to new
 files with --keep argument

* remove ifort switches that issue warnings
* write absolute zip file path if using --zip argument
---
 pymake/pymake.py                   | 21 ++++++++++++++++++---
 pymake/utils/_compiler_switches.py |  3 ---
 2 files changed, 18 insertions(+), 6 deletions(-)

diff --git a/pymake/pymake.py b/pymake/pymake.py
index 22ab447..e79b3f3 100644
--- a/pymake/pymake.py
+++ b/pymake/pymake.py
@@ -58,6 +58,7 @@
 import shutil
 import sys
 import time
+from zipfile import ZipFile
 
 from .config import __description__
 from .pymake_base import main
@@ -267,18 +268,32 @@ def compress_targets(self):
                     if self.verbose:
                         print(
                             "Appending files to existing "
-                            + f"zipfile '{zip_pth}'"
+                            + f"zipfile '{pl.Path(zip_pth).resolve()}'"
                         )
+                    with ZipFile(
+                        zip_pth,
+                        mode="r",
+                    ) as zf:
+                        available_file_paths = zf.namelist()
+                        pop_list = []
+                        for target in targets:
+                            if target in available_file_paths:
+                                pop_list.append(target)
+                            for target in pop_list:
+                                targets.remove(target)
                 else:
                     if self.verbose:
-                        print(f"Deleting existing zipfile '{zip_pth}'")
+                        print(
+                            "Deleting existing zipfile "
+                            + f"'{pl.Path(zip_pth).resolve()}'"
+                        )
                     os.remove(zip_pth)
 
             # print a message describing the zip process
             if self.verbose:
                 print(
                     f"Compressing files in '{appdir}' "
-                    + f"directory to zip file '{zip_pth}'"
+                    + f"directory to zip file '{pl.Path(zip_pth).resolve()}'"
                 )
                 for idx, target in enumerate(targets):
                     print(
diff --git a/pymake/utils/_compiler_switches.py b/pymake/utils/_compiler_switches.py
index 21c7ad7..975d862 100644
--- a/pymake/utils/_compiler_switches.py
+++ b/pymake/utils/_compiler_switches.py
@@ -339,9 +339,6 @@ def _get_fortran_flags(
                     "fpe:0",
                     "traceback",
                     "nologo",
-                    "Qdiag-disable:7416",
-                    "Qdiag-disable:7025",
-                    "Qdiag-disable:5268",
                 ]
                 if debug:
                     flags += ["debug:full", "Zi"]

From 813e0823365b4a659f221d8761d43f61e457c63b Mon Sep 17 00:00:00 2001
From: Joseph D Hughes <jdhughes@usgs.gov>
Date: Thu, 15 Feb 2024 11:34:34 -0600
Subject: [PATCH 2/2] * codeacy fix

---
 pymake/pymake.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pymake/pymake.py b/pymake/pymake.py
index e79b3f3..0c85933 100644
--- a/pymake/pymake.py
+++ b/pymake/pymake.py
@@ -279,8 +279,8 @@ def compress_targets(self):
                         for target in targets:
                             if target in available_file_paths:
                                 pop_list.append(target)
-                            for target in pop_list:
-                                targets.remove(target)
+                        for target in pop_list:
+                            targets.remove(target)
                 else:
                     if self.verbose:
                         print(