From 2747385f89bfb52db638a37457c1dfae0a27f246 Mon Sep 17 00:00:00 2001
From: kba <unixprog@gmail.com>
Date: Thu, 7 May 2026 17:15:15 +0200
Subject: [PATCH 1/3] remove unused deprecating-warning-causing biopyton
 dependency

---
 requirements.txt                | 1 -
 src/eynollah/utils/utils_ocr.py | 6 ------
 2 files changed, 7 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index 53d1e39..d79853f 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -6,5 +6,4 @@ tensorflow
 tf-keras # avoid keras 3 (also needs TF_USE_LEGACY_KERAS=1)
 numba <= 0.58.1
 scikit-image
-biopython
 tabulate
diff --git a/src/eynollah/utils/utils_ocr.py b/src/eynollah/utils/utils_ocr.py
index 928c164..93d1137 100644
--- a/src/eynollah/utils/utils_ocr.py
+++ b/src/eynollah/utils/utils_ocr.py
@@ -7,7 +7,6 @@ import tensorflow as tf
 from scipy.signal import find_peaks
 from scipy.ndimage import gaussian_filter1d
 from PIL import Image, ImageDraw, ImageFont
-from Bio import pairwise2
 
 from .resize import resize_image
 
@@ -503,8 +502,3 @@ def return_rnn_cnn_ocr_of_given_textlines(image,
             ocr_textline_in_textregion.append(text_textline)
         ocr_all_textlines.append(ocr_textline_in_textregion)
     return ocr_all_textlines
-
-def biopython_align(str1, str2):
-    alignments = pairwise2.align.globalms(str1, str2, 2, -1, -2, -2)
-    best_alignment = alignments[0]  # Get the best alignment
-    return best_alignment.seqA, best_alignment.seqB

From 34a9d458ce7723006d6e5ccb48045d396738d254 Mon Sep 17 00:00:00 2001
From: kba <unixprog@gmail.com>
Date: Thu, 7 May 2026 18:09:27 +0200
Subject: [PATCH 2/3] training deps: use sacred fork w/o pkg_resources, pin
 tf/tf_keras, protobuf packages to work with tensorflow_addons

---
 train/requirements.txt | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/train/requirements.txt b/train/requirements.txt
index 6f23d76..090bc50 100644
--- a/train/requirements.txt
+++ b/train/requirements.txt
@@ -1,7 +1,10 @@
-sacred
+ocrd-fork-sacred >= 0.8.7.post1
 seaborn
 numpy
 tqdm
 imutils
 scipy
-tensorflow-addons # for connected_components
+tensorflow-addons # for connected_components, depublished and only compatible with tensorflow < 2.16
+tensorflow < 2.16 # for tensorflow-addons, so only needed in training
+tf_data < 2.16 # for tensorflow-addons, so only needed in training
+protobuf < 5 # for tensorflow-addons, so only needed in training

From a0bf1b51f4b10716f69d46fa5ad517ae9008eadf Mon Sep 17 00:00:00 2001
From: kba <unixprog@gmail.com>
Date: Thu, 7 May 2026 19:30:29 +0200
Subject: [PATCH 3/3] makefile to reload models

---
 src/eynollah/training/reload-models-v0.8.mk | 48 +++++++++++++++++++++
 1 file changed, 48 insertions(+)
 create mode 100644 src/eynollah/training/reload-models-v0.8.mk

diff --git a/src/eynollah/training/reload-models-v0.8.mk b/src/eynollah/training/reload-models-v0.8.mk
new file mode 100644
index 0000000..b7a38dd
--- /dev/null
+++ b/src/eynollah/training/reload-models-v0.8.mk
@@ -0,0 +1,48 @@
+SHELL = bash -e
+
+MODELS_SRC = models_eynollah
+MODELS_DST = reloaded/models_eynollah
+
+
+#	$(MODELS_DST)/eynollah-binarization_20210425 \
+#	$(MODELS_DST)/eynollah-column-classifier_20210425 \
+#	$(MODELS_DST)/eynollah-enhancement_20210425 \
+#	$(MODELS_DST)/eynollah-main-regions-aug-rotation_20210425 \
+#	$(MODELS_DST)/eynollah-main-regions-aug-scaling_20210425 \
+#	$(MODELS_DST)/eynollah-main-regions-ensembled_20210425 \
+#	$(MODELS_DST)/eynollah-main-regions_20220314 \
+#	$(MODELS_DST)/eynollah-main-regions_20231127_672_org_ens_11_13_16_17_18 \
+#	$(MODELS_DST)/eynollah-tables_20210319 \
+#	$(MODELS_DST)/model_eynollah_ocr_cnnrnn_20250930 \
+
+RELOADABLE_MODELS = \
+	$(MODELS_DST)/model_eynollah_page_extraction_20250915 \
+	$(MODELS_DST)/model_eynollah_reading_order_20250824 \
+	$(MODELS_DST)/modelens_e_l_all_sp_0_1_2_3_4_171024 \
+	$(MODELS_DST)/modelens_full_lay_1__4_3_091124 \
+	$(MODELS_DST)/modelens_table_0t4_201124 \
+	$(MODELS_DST)/modelens_textline_0_1__2_4_16092024
+
+all: $(RELOADABLE_MODELS)
+
+$(MODELS_DST)/%: $(MODELS_SRC)/%
+	mkdir -p $@
+	test -e $</config.json || exit 1
+	eynollah-training train --force \
+		with $</config.json \
+		reload_weights=True \
+		continue_training=False \
+		dir_output=$(dir $@) \
+		dir_of_start_model=$< \
+	2>&1 | tee $(notdir $<).log
+	cp $</config.json $@/config.json
+
+compare: 
+	for i in `find $(MODELS_DST) -mindepth 2`;do \
+	 	n=$(MODELS_SRC)$${i#$(MODELS_DST)}; \
+		du -bs $$n $$i ; \
+	done
+
+
+clear:
+	rm -rf $(MODELS_DST)