v1.3 large update

-v 1.1 beta, January 2021
+v 1.3 beta, January 2021
 
 
 The first uses of RNAnet by people from outside the development team happened between this December.
 The first uses of RNAnet by people from outside the development team happened between this December.
 A few feedback allowed to identify issues and useful information to add.
 A few feedback allowed to identify issues and useful information to add.
 
 
 FEATURE CHANGES
 FEATURE CHANGES
-    - Sequence alignments of the 3D structures mapped to a family are now provided. 
+    - Sequence alignments of the 3D structures mapped to a family are now provided.
     - Full alignements with Rfam sequences are not provided, but you can ask us for the files.
     - Full alignements with Rfam sequences are not provided, but you can ask us for the files.
     - Two new fields in table 'family': ali_length and ali_filtered_length. 
     - Two new fields in table 'family': ali_length and ali_filtered_length. 
     They are the MSA lengths of the alignment with and without the Rfam sequences. 
     They are the MSA lengths of the alignment with and without the Rfam sequences. 
+    - Gap replacement by consensus (--fill-gaps) has been removed. Now, the gap percentage and consensus are saved 
+    in the align_column table and the datapoints in CSV format, in separate columns. 
+    Consensus is one of ACGUN-, the gap being chosen if >75% of the sequences are gaps at this position. 
+    Otherwise, A/C/G/U is chosen if >50% of the non-gap positions are A/C/G/U. Otherwise, N is the consensus.
 
 
 TECHNICAL CHANGES
 TECHNICAL CHANGES
-    - SQLite connexions are now all in WAL mode by default (previously, only the writers used WAL mode)
+    - SQLite connexions are now all in WAL mode by default (previously, only the writers used WAL mode, but this is useless)
+    - Moved to Python3.9 for internal testing.
+    - Latest version of BioPython is now supported (1.78)
 
 
 BUG CORRECTIONS
 BUG CORRECTIONS
     - When an alignment file is updated in a newer run of RNANet, all the re_mappings are now re-computed 
     - When an alignment file is updated in a newer run of RNANet, all the re_mappings are now re-computed 
@@ -19,8 +25,8 @@ BUG CORRECTIONS
     - Changed the ownership and permissions of files produced by the Docker container. 
     - Changed the ownership and permissions of files produced by the Docker container. 
     They were previously owned by root and the user could not get access to them.
     They were previously owned by root and the user could not get access to them.
     - Modified nucleotides were not always correctly transformed to N in the alignments (and nucleotide.nt_align_code fields).
     - Modified nucleotides were not always correctly transformed to N in the alignments (and nucleotide.nt_align_code fields).
-    Now, the alignments and nt_align_code only contain "ACGUN-" chars. 
-    Now, 'N' means 'other', while '-' means 'nothing'.
+    Now, the alignments and nt_align_code (and consensus) only contain "ACGUN-" chars. 
+    Now, 'N' means 'other', while '-' means 'nothing' or 'unknown'.
 
 
 COMING SOON
 COMING SOON
     - Automated annotation of detected Recurrent Interaction Networks (RINs), see http://carnaval.lri.fr/ .
     - Automated annotation of detected Recurrent Interaction Networks (RINs), see http://carnaval.lri.fr/ .

@@ -14,7 +14,7 @@ RUN apk update && apk add --no-cache \
         py3-matplotlib py3-requests py3-scipy py3-setproctitle py3-sqlalchemy py3-tqdm \
         py3-matplotlib py3-requests py3-scipy py3-setproctitle py3-sqlalchemy py3-tqdm \
         sqlite \
         sqlite \
     \
     \
-    && python3 -m pip install biopython==1.76 pandas psutil pymysql && \
+    && python3 -m pip install biopython pandas psutil pymysql && \
     \
     \
     wget -q -O /etc/apk/keys/sgerrand.rsa.pub https://alpine-pkgs.sgerrand.com/sgerrand.rsa.pub && \
     wget -q -O /etc/apk/keys/sgerrand.rsa.pub https://alpine-pkgs.sgerrand.com/sgerrand.rsa.pub && \
     wget https://github.com/sgerrand/alpine-pkg-glibc/releases/download/2.32-r0/glibc-2.32-r0.apk && \
     wget https://github.com/sgerrand/alpine-pkg-glibc/releases/download/2.32-r0/glibc-2.32-r0.apk && \