From 60829eebd2ac65d21e93c55d53394308ccb99690 Mon Sep 17 00:00:00 2001
From: "Jose M. de la Rosa" <delarosatrevin@gmail.com>
Date: Mon, 26 Feb 2024 16:06:12 -0600
Subject: [PATCH 1/3] Minor update of inputCount in SetMonitor

---
 emtools/pwx/monitors.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/emtools/pwx/monitors.py b/emtools/pwx/monitors.py
index 79e3d8d..28f1b43 100644
--- a/emtools/pwx/monitors.py
+++ b/emtools/pwx/monitors.py
@@ -123,6 +123,7 @@ def __init__(self, SetClass, filename, *args, **kwargs):
         self._filename = filename
         self.lastUpdate = None
         self.streamClosed = None
+        self.inputCount = 0  # Count all input elements
 
         # Black list some items to not be monitored again
         # We are not interested in the items but just skip them from
@@ -141,6 +142,7 @@ def update(self):
             setInstance = self._SetClass(filename=self._filename)
             setInstance.loadAllProperties()
             for item in setInstance.iterItems():
+                self.inputCount += 1
                 iid = item.getObjId()
                 if iid not in self:
                     itemClone = item.clone()
@@ -170,10 +172,10 @@ def iterProtocolInput(self, prot, label, waitSecs=60):
         else:
             prot.info(f"No output {label}.")
 
-        for newMovie in self.newItems(sleep=waitSecs):
-            yield newMovie
+        for newItem in self.newItems(sleep=waitSecs):
+            yield newItem
 
-        prot.info(f"No more movies, stream closed. Total: {len(self)}")
+        prot.info(f"No more {label}, stream closed. Total: {len(self)}")
 
 
 class BatchManager:

From 57d22f02237a40b0bf2da5279fb23ef97fb29032 Mon Sep 17 00:00:00 2001
From: "Jose M. de la Rosa" <delarosatrevin@gmail.com>
Date: Sun, 3 Mar 2024 11:02:39 -0600
Subject: [PATCH 2/3] Minor update in Scipion OTF script

---
 emtools/scripts/emt-scipion-otf.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/emtools/scripts/emt-scipion-otf.py b/emtools/scripts/emt-scipion-otf.py
index 6acbfff..6155cdf 100755
--- a/emtools/scripts/emt-scipion-otf.py
+++ b/emtools/scripts/emt-scipion-otf.py
@@ -431,7 +431,7 @@ def continue_project(workingDir):
         print(f"Run {run.getObjId()}: {clsName}")
         if clsName == 'ProtRelionExtractParticles':
             protExtract = run
-        elif clsName == 'SphireProtCRYOLOPicking':
+        elif clsName.startswith('SphireProtCRYOLOPicking'):
             protCryolo = run
 
     if not protExtract.isActive():
@@ -629,7 +629,11 @@ def _get_keys(tokens):
                 protPicking = prot
 
     if protCtf:
-        ctfs = protCtf.outputCTF
+        if hasattr(protCtf, 'outputCTF'):
+            ctfs = protCtf.outputCTF
+        else: 
+            ctfs = protCtf.outputSet  # case of union, FIXME: validate other non-valid
+
         print_prot(protCtf, label='CTF protocol')
         print(f"            CTFs: {ctfs.getSize()}")
         write_micrographs_star('micrographs_ctf.star', ctfs)

From b69c53e2c350fb73d981e0c1df5dbae0f05e54ba Mon Sep 17 00:00:00 2001
From: "J.M de la Rosa Trevin" <delarosatrevin@gmail.com>
Date: Sun, 3 Mar 2024 11:06:14 -0600
Subject: [PATCH 3/3] Updated version and publish workflow

---
 .github/workflows/publish_and_tag.yml | 4 ++--
 emtools/__init__.py                   | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/publish_and_tag.yml b/.github/workflows/publish_and_tag.yml
index 5735587..698e6f7 100644
--- a/.github/workflows/publish_and_tag.yml
+++ b/.github/workflows/publish_and_tag.yml
@@ -27,8 +27,8 @@ jobs:
         pip install setuptools wheel twine
     - name: Build and publish
       env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        TWINE_USERNAME: ${{ __token__ }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_JMRT_TOKEN }}
       run: |
         python setup.py sdist bdist_wheel
         twine upload dist/*
diff --git a/emtools/__init__.py b/emtools/__init__.py
index f0c9a67..3fc9a10 100644
--- a/emtools/__init__.py
+++ b/emtools/__init__.py
@@ -24,5 +24,5 @@
 # *
 # **************************************************************************
 
-__version__ = '0.0.10'
+__version__ = '0.0.11'